Starting phenix.real_space_refine on Sat May 17 18:41:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3s_36858/05_2025/8k3s_36858_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3s_36858/05_2025/8k3s_36858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3s_36858/05_2025/8k3s_36858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3s_36858/05_2025/8k3s_36858.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3s_36858/05_2025/8k3s_36858_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3s_36858/05_2025/8k3s_36858_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15761 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {' CA': 1, 'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.55, per 1000 atoms: 0.61 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: 4.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.59 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: 4.40 Time building geometry restraints manager: 4.82 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 686 or resid 801 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.670 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.830 16196 Z= 0.939 Angle : 0.760 16.047 21960 Z= 0.407 Chirality : 0.044 0.283 2456 Planarity : 0.006 0.129 2696 Dihedral : 14.320 89.967 5992 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.77 % Allowed : 1.18 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (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 TRP 0.017 0.001 TRP D 414 HIS 0.004 0.001 HIS B 379 PHE 0.033 0.001 PHE C 600 TYR 0.017 0.001 TYR D 249 ARG 0.006 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 12) link_NAG-ASN : angle 1.56814 ( 36) hydrogen bonds : bond 0.16868 ( 797) hydrogen bonds : angle 5.92567 ( 2415) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.81740 ( 8) covalent geometry : bond 0.00385 (16176) covalent geometry : angle 0.75717 (21916) Misc. bond : bond 0.58516 ( 4) *********************** 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 : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.6266 (pmm) cc_final: 0.5385 (tpt) REVERT: A 684 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.3338 (m-10) REVERT: B 583 MET cc_start: 0.5745 (pmm) cc_final: 0.5064 (tpt) REVERT: B 585 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: B 684 TYR cc_start: 0.5583 (OUTLIER) cc_final: 0.4750 (t80) REVERT: C 227 TYR cc_start: 0.7810 (t80) cc_final: 0.7604 (t80) REVERT: C 495 ILE cc_start: 0.8127 (tt) cc_final: 0.7911 (mt) REVERT: C 508 ASN cc_start: 0.8504 (m110) cc_final: 0.8196 (m-40) REVERT: C 583 MET cc_start: 0.5902 (pmm) cc_final: 0.5163 (tpt) REVERT: D 508 ASN cc_start: 0.8519 (m110) cc_final: 0.8296 (m-40) REVERT: D 583 MET cc_start: 0.6227 (pmm) cc_final: 0.5298 (tpt) outliers start: 13 outliers final: 6 residues processed: 353 average time/residue: 0.9958 time to fit residues: 396.5226 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 : 1.586 ------------------------------------------------------------------------------- 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 155 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 543 ASN B 305 ASN B 412 ASN B 543 ASN C 305 ASN C 412 ASN C 543 ASN D 305 ASN D 379 HIS D 412 ASN D 543 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113876 restraints weight = 18475.124| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.28 r_work: 0.3159 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16196 Z= 0.125 Angle : 0.590 7.406 21960 Z= 0.315 Chirality : 0.041 0.177 2456 Planarity : 0.006 0.192 2696 Dihedral : 9.895 87.508 2477 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 2.67 % Allowed : 11.67 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1848 helix: 1.17 (0.17), residues: 972 sheet: -0.91 (0.38), residues: 200 loop : -1.78 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 414 HIS 0.002 0.001 HIS D 498 PHE 0.022 0.001 PHE D 670 TYR 0.017 0.001 TYR A 249 ARG 0.026 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 12) link_NAG-ASN : angle 1.63080 ( 36) hydrogen bonds : bond 0.04565 ( 797) hydrogen bonds : angle 4.13170 ( 2415) SS BOND : bond 0.00362 ( 4) SS BOND : angle 2.04983 ( 8) covalent geometry : bond 0.00263 (16176) covalent geometry : angle 0.58534 (21916) Misc. bond : bond 0.00215 ( 4) *********************** 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 328 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7929 (t80) cc_final: 0.7653 (t80) REVERT: A 236 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8838 (tp) REVERT: A 305 ASN cc_start: 0.7420 (p0) cc_final: 0.7054 (p0) REVERT: A 590 MET cc_start: 0.7049 (mmp) cc_final: 0.6784 (mmt) REVERT: A 602 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (pp) REVERT: A 684 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.3166 (m-10) REVERT: B 229 LEU cc_start: 0.8559 (mt) cc_final: 0.8295 (mp) REVERT: B 583 MET cc_start: 0.6097 (pmm) cc_final: 0.5276 (tpt) REVERT: B 586 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6600 (OUTLIER) REVERT: C 229 LEU cc_start: 0.8498 (mt) cc_final: 0.8245 (mp) REVERT: C 255 GLN cc_start: 0.8753 (mt0) cc_final: 0.8515 (mt0) REVERT: C 305 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6933 (p0) REVERT: C 508 ASN cc_start: 0.8560 (m110) cc_final: 0.8251 (m-40) REVERT: C 583 MET cc_start: 0.5908 (pmm) cc_final: 0.5058 (tpt) REVERT: C 590 MET cc_start: 0.4863 (mtp) cc_final: 0.3808 (mmt) REVERT: D 583 MET cc_start: 0.5736 (pmm) cc_final: 0.5062 (tpt) outliers start: 45 outliers final: 10 residues processed: 304 average time/residue: 0.8196 time to fit residues: 288.3552 Evaluate side-chains 251 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE 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 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 305 ASN Chi-restraints excluded: chain C residue 482 PHE 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 56 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN B 580 ASN C 305 ASN C 543 ASN D 305 ASN D 543 ASN ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106467 restraints weight = 18542.669| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.27 r_work: 0.3051 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16196 Z= 0.245 Angle : 0.711 7.645 21960 Z= 0.376 Chirality : 0.047 0.190 2456 Planarity : 0.005 0.120 2696 Dihedral : 9.439 89.536 2464 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.76 % Favored : 93.02 % Rotamer: Outliers : 4.27 % Allowed : 14.40 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1848 helix: 1.03 (0.17), residues: 984 sheet: -1.07 (0.36), residues: 200 loop : -1.64 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 414 HIS 0.004 0.001 HIS D 498 PHE 0.021 0.002 PHE B 600 TYR 0.028 0.002 TYR A 249 ARG 0.014 0.001 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 12) link_NAG-ASN : angle 2.30204 ( 36) hydrogen bonds : bond 0.05982 ( 797) hydrogen bonds : angle 4.17539 ( 2415) SS BOND : bond 0.00752 ( 4) SS BOND : angle 3.52901 ( 8) covalent geometry : bond 0.00593 (16176) covalent geometry : angle 0.70258 (21916) Misc. bond : bond 0.00248 ( 4) *********************** 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 334 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 262 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8193 (mpp) REVERT: A 305 ASN cc_start: 0.7478 (p0) cc_final: 0.7019 (p0) REVERT: A 583 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.4838 (tpt) REVERT: A 631 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 651 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 680 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.7012 (mm) REVERT: A 684 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.3188 (m-10) REVERT: B 252 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8132 (mpp) REVERT: B 305 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6781 (p0) REVERT: B 583 MET cc_start: 0.6265 (pmm) cc_final: 0.5384 (tpt) REVERT: B 602 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8092 (pp) REVERT: B 651 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: C 252 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8170 (mpp) REVERT: C 255 GLN cc_start: 0.8873 (mt0) cc_final: 0.8654 (mt0) REVERT: C 305 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6561 (p0) REVERT: C 583 MET cc_start: 0.5980 (pmm) cc_final: 0.4756 (tpt) REVERT: C 590 MET cc_start: 0.4860 (mtp) cc_final: 0.4289 (mtm) REVERT: C 603 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7513 (ttt) REVERT: C 650 GLU cc_start: 0.8401 (tp30) cc_final: 0.7826 (pt0) REVERT: C 651 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: D 252 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8128 (mpp) REVERT: D 305 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6677 (p0) REVERT: D 538 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7872 (t80) REVERT: D 583 MET cc_start: 0.5842 (pmm) cc_final: 0.5044 (tpt) REVERT: D 602 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7886 (pp) REVERT: D 603 MET cc_start: 0.7949 (ttt) cc_final: 0.7745 (ttt) REVERT: D 631 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7436 (mt-10) outliers start: 72 outliers final: 18 residues processed: 294 average time/residue: 0.8682 time to fit residues: 292.9085 Evaluate side-chains 278 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 680 ILE 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 425 ASP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 684 TYR 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 538 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 ASN C 543 ASN D 305 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 = 0.3837 r_free = 0.3837 target = 0.159087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110215 restraints weight = 18353.988| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.26 r_work: 0.3095 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2114 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= 0.140 Angle : 0.605 7.539 21960 Z= 0.323 Chirality : 0.042 0.162 2456 Planarity : 0.006 0.207 2696 Dihedral : 8.925 88.677 2462 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 3.14 % Allowed : 17.12 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1848 helix: 1.33 (0.17), residues: 960 sheet: -1.04 (0.37), residues: 200 loop : -1.64 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 414 HIS 0.002 0.001 HIS D 498 PHE 0.022 0.001 PHE A 670 TYR 0.018 0.001 TYR B 527 ARG 0.020 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 12) link_NAG-ASN : angle 1.74824 ( 36) hydrogen bonds : bond 0.04827 ( 797) hydrogen bonds : angle 3.92443 ( 2415) SS BOND : bond 0.00457 ( 4) SS BOND : angle 2.65327 ( 8) covalent geometry : bond 0.00311 (16176) covalent geometry : angle 0.59954 (21916) Misc. bond : bond 0.00295 ( 4) *********************** 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 321 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7964 (t80) cc_final: 0.7543 (t80) REVERT: A 255 GLN cc_start: 0.8828 (mt0) cc_final: 0.8607 (mt0) REVERT: A 305 ASN cc_start: 0.7432 (p0) cc_final: 0.7044 (p0) REVERT: A 583 MET cc_start: 0.6062 (pmt) cc_final: 0.4786 (tpt) REVERT: A 590 MET cc_start: 0.6502 (mmt) cc_final: 0.5970 (ptt) REVERT: A 602 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7973 (pp) REVERT: A 631 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7240 (mt-10) REVERT: A 651 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: A 684 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.3129 (m-10) REVERT: B 227 TYR cc_start: 0.8048 (t80) cc_final: 0.7482 (t80) REVERT: B 251 ARG cc_start: 0.8866 (ttt90) cc_final: 0.8603 (ttt90) REVERT: B 252 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8120 (mpp) REVERT: B 305 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6499 (p0) REVERT: B 583 MET cc_start: 0.6320 (pmm) cc_final: 0.5432 (tpt) REVERT: B 651 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: C 252 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: C 255 GLN cc_start: 0.8768 (mt0) cc_final: 0.8567 (mt0) REVERT: C 305 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6520 (p0) REVERT: C 583 MET cc_start: 0.6063 (pmm) cc_final: 0.5029 (tpt) REVERT: C 590 MET cc_start: 0.4677 (mtp) cc_final: 0.4036 (mtm) REVERT: C 602 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7742 (pp) REVERT: C 603 MET cc_start: 0.7562 (ttp) cc_final: 0.7149 (ttt) REVERT: C 651 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: D 251 ARG cc_start: 0.8905 (ttt90) cc_final: 0.8654 (ttt90) REVERT: D 252 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8111 (mpp) REVERT: D 305 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6845 (p0) REVERT: D 583 MET cc_start: 0.5697 (pmm) cc_final: 0.4849 (tpt) outliers start: 53 outliers final: 15 residues processed: 289 average time/residue: 0.9137 time to fit residues: 301.3904 Evaluate side-chains 268 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain 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 425 ASP Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 28 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 ASN C 543 ASN D 305 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 = 0.3839 r_free = 0.3839 target = 0.159193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109926 restraints weight = 18651.344| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.26 r_work: 0.3088 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16196 Z= 0.147 Angle : 0.612 8.838 21960 Z= 0.325 Chirality : 0.042 0.153 2456 Planarity : 0.005 0.121 2696 Dihedral : 8.626 87.297 2462 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.03 % Favored : 92.75 % Rotamer: Outliers : 3.91 % Allowed : 17.36 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1848 helix: 1.37 (0.17), residues: 964 sheet: -1.03 (0.37), residues: 200 loop : -1.66 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 414 HIS 0.002 0.001 HIS D 498 PHE 0.021 0.001 PHE B 600 TYR 0.016 0.001 TYR B 527 ARG 0.013 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 12) link_NAG-ASN : angle 1.75620 ( 36) hydrogen bonds : bond 0.04787 ( 797) hydrogen bonds : angle 3.87623 ( 2415) SS BOND : bond 0.00493 ( 4) SS BOND : angle 2.62788 ( 8) covalent geometry : bond 0.00333 (16176) covalent geometry : angle 0.60598 (21916) Misc. bond : bond 0.00178 ( 4) *********************** 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 321 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7960 (t80) cc_final: 0.7580 (t80) REVERT: A 252 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8184 (mpp) REVERT: A 255 GLN cc_start: 0.8823 (mt0) cc_final: 0.8599 (mt0) REVERT: A 305 ASN cc_start: 0.7367 (p0) cc_final: 0.6909 (p0) REVERT: A 583 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.4732 (tpt) REVERT: A 590 MET cc_start: 0.6617 (mmt) cc_final: 0.6140 (ptm) REVERT: A 602 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7653 (pp) REVERT: A 631 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 651 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: A 684 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.3115 (m-10) REVERT: B 251 ARG cc_start: 0.8878 (ttt90) cc_final: 0.8625 (ttt90) REVERT: B 252 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8081 (mpp) REVERT: B 305 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6443 (p0) REVERT: B 583 MET cc_start: 0.6201 (pmm) cc_final: 0.5121 (tpt) REVERT: B 602 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7965 (pp) REVERT: B 651 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: C 252 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8105 (mpp) REVERT: C 305 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6308 (p0) REVERT: C 583 MET cc_start: 0.6109 (pmm) cc_final: 0.4950 (tpt) REVERT: C 590 MET cc_start: 0.4694 (mtp) cc_final: 0.3730 (ptm) REVERT: C 602 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7774 (pp) REVERT: C 603 MET cc_start: 0.7586 (ttp) cc_final: 0.7091 (ttt) REVERT: C 651 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: D 251 ARG cc_start: 0.8913 (ttt90) cc_final: 0.8671 (ttt90) REVERT: D 252 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8130 (mpp) REVERT: D 305 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6766 (p0) REVERT: D 538 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7785 (t80) REVERT: D 583 MET cc_start: 0.5850 (pmm) cc_final: 0.4869 (tpt) REVERT: D 590 MET cc_start: 0.5950 (ptt) cc_final: 0.5152 (ppp) REVERT: D 603 MET cc_start: 0.7469 (ttp) cc_final: 0.6959 (ttt) REVERT: D 631 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7344 (mt-10) outliers start: 66 outliers final: 27 residues processed: 286 average time/residue: 0.8961 time to fit residues: 293.5662 Evaluate side-chains 279 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET 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 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 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 305 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 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 425 ASP Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 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 31 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 ASN C 543 ASN D 305 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 = 0.3875 r_free = 0.3875 target = 0.162518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113227 restraints weight = 18609.622| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.29 r_work: 0.3137 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2267 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= 0.115 Angle : 0.570 10.525 21960 Z= 0.303 Chirality : 0.041 0.144 2456 Planarity : 0.004 0.073 2696 Dihedral : 8.204 88.240 2462 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.60 % Favored : 93.18 % Rotamer: Outliers : 2.96 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1848 helix: 1.55 (0.17), residues: 956 sheet: -0.95 (0.37), residues: 200 loop : -1.66 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 414 HIS 0.001 0.000 HIS D 498 PHE 0.025 0.001 PHE A 670 TYR 0.015 0.001 TYR B 527 ARG 0.007 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 12) link_NAG-ASN : angle 1.53378 ( 36) hydrogen bonds : bond 0.04143 ( 797) hydrogen bonds : angle 3.74474 ( 2415) SS BOND : bond 0.00239 ( 4) SS BOND : angle 2.02303 ( 8) covalent geometry : bond 0.00243 (16176) covalent geometry : angle 0.56583 (21916) Misc. bond : bond 0.00115 ( 4) *********************** 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 305 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 1.777 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: 0.7914 (t80) cc_final: 0.7571 (t80) REVERT: A 255 GLN cc_start: 0.8811 (mt0) cc_final: 0.8506 (mt0) REVERT: A 305 ASN cc_start: 0.7320 (p0) cc_final: 0.6937 (p0) REVERT: A 583 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.4624 (tpt) REVERT: A 590 MET cc_start: 0.6717 (mmt) cc_final: 0.6342 (pp-130) REVERT: A 631 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 651 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: A 684 TYR cc_start: 0.5018 (OUTLIER) cc_final: 0.3142 (m-10) REVERT: B 251 ARG cc_start: 0.8803 (ttt90) cc_final: 0.8582 (ttt90) REVERT: B 252 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8164 (mpp) REVERT: B 305 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6586 (p0) REVERT: B 343 GLU cc_start: 0.8496 (mp0) cc_final: 0.7960 (mm-30) REVERT: B 455 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.7719 (p90) REVERT: B 583 MET cc_start: 0.5853 (pmm) cc_final: 0.4915 (tpp) REVERT: B 590 MET cc_start: 0.3837 (mtp) cc_final: 0.3226 (mtm) REVERT: B 602 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7834 (pp) REVERT: B 651 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: C 251 ARG cc_start: 0.8869 (ttt90) cc_final: 0.8635 (ttt90) REVERT: C 252 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: C 305 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6252 (p0) REVERT: C 583 MET cc_start: 0.5950 (pmm) cc_final: 0.4796 (tpt) REVERT: C 590 MET cc_start: 0.4643 (mtp) cc_final: 0.3553 (ptm) REVERT: C 603 MET cc_start: 0.7548 (ttp) cc_final: 0.7092 (ttt) REVERT: C 651 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: D 251 ARG cc_start: 0.8843 (ttt90) cc_final: 0.8619 (ttt90) REVERT: D 252 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8159 (mpp) REVERT: D 305 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.6802 (p0) REVERT: D 538 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7831 (t80) REVERT: D 583 MET cc_start: 0.5838 (pmm) cc_final: 0.4864 (tpt) REVERT: D 590 MET cc_start: 0.6029 (ptt) cc_final: 0.5135 (ppp) REVERT: D 602 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7652 (pp) REVERT: D 603 MET cc_start: 0.7360 (ttp) cc_final: 0.7049 (ttm) REVERT: D 631 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7322 (mt-10) outliers start: 50 outliers final: 17 residues processed: 275 average time/residue: 0.8920 time to fit residues: 281.2085 Evaluate side-chains 275 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 A residue 651 GLU 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 305 ASN 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 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 425 ASP Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 0.0020 chunk 138 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 ASN C 543 ASN D 305 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 = 0.3868 r_free = 0.3868 target = 0.161801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112569 restraints weight = 18565.306| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.28 r_work: 0.3138 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16196 Z= 0.125 Angle : 0.593 8.218 21960 Z= 0.313 Chirality : 0.042 0.176 2456 Planarity : 0.005 0.203 2696 Dihedral : 8.078 86.083 2462 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.98 % Favored : 92.80 % Rotamer: Outliers : 2.96 % Allowed : 19.08 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1848 helix: 1.60 (0.17), residues: 956 sheet: -0.90 (0.37), residues: 200 loop : -1.60 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.002 0.001 HIS B 379 PHE 0.022 0.001 PHE B 600 TYR 0.014 0.001 TYR B 527 ARG 0.016 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 12) link_NAG-ASN : angle 1.57404 ( 36) hydrogen bonds : bond 0.04240 ( 797) hydrogen bonds : angle 3.72161 ( 2415) SS BOND : bond 0.00353 ( 4) SS BOND : angle 1.90134 ( 8) covalent geometry : bond 0.00273 (16176) covalent geometry : angle 0.58880 (21916) Misc. bond : bond 0.00235 ( 4) *********************** 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 299 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 1.800 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: 0.7925 (t80) cc_final: 0.7590 (t80) REVERT: A 252 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8152 (mpp) REVERT: A 255 GLN cc_start: 0.8824 (mt0) cc_final: 0.8536 (mt0) REVERT: A 305 ASN cc_start: 0.7329 (p0) cc_final: 0.6865 (p0) REVERT: A 583 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.4726 (tpt) REVERT: A 590 MET cc_start: 0.6683 (mmt) cc_final: 0.6363 (pp-130) REVERT: A 631 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 651 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: B 251 ARG cc_start: 0.8830 (ttt90) cc_final: 0.8596 (ttt90) REVERT: B 252 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: B 305 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6517 (p0) REVERT: B 312 GLU cc_start: 0.8143 (pm20) cc_final: 0.7910 (pm20) REVERT: B 455 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.7641 (p90) REVERT: B 583 MET cc_start: 0.5858 (pmm) cc_final: 0.4914 (tpp) REVERT: B 590 MET cc_start: 0.3988 (mtp) cc_final: 0.3344 (mtm) REVERT: B 602 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7854 (pp) REVERT: C 251 ARG cc_start: 0.8873 (ttt90) cc_final: 0.8668 (ttt90) REVERT: C 252 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: C 305 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6348 (p0) REVERT: C 583 MET cc_start: 0.5904 (pmm) cc_final: 0.4798 (tpt) REVERT: C 590 MET cc_start: 0.4741 (mtp) cc_final: 0.3455 (ptm) REVERT: C 603 MET cc_start: 0.7570 (ttp) cc_final: 0.7062 (ttt) REVERT: C 651 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: D 251 ARG cc_start: 0.8848 (ttt90) cc_final: 0.8611 (ttt90) REVERT: D 252 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: D 305 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.6878 (p0) REVERT: D 538 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7862 (t80) REVERT: D 583 MET cc_start: 0.5893 (pmm) cc_final: 0.5050 (tpt) REVERT: D 590 MET cc_start: 0.5932 (ptt) cc_final: 0.5098 (ppp) REVERT: D 602 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7684 (pp) REVERT: D 603 MET cc_start: 0.7375 (ttp) cc_final: 0.6836 (ttt) outliers start: 50 outliers final: 21 residues processed: 267 average time/residue: 0.9342 time to fit residues: 286.7738 Evaluate side-chains 269 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU 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 252 MET Chi-restraints excluded: chain C residue 305 ASN 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 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 425 ASP Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 156 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 166 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 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 = 0.3863 r_free = 0.3863 target = 0.161309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112056 restraints weight = 18309.602| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.27 r_work: 0.3132 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16196 Z= 0.131 Angle : 0.600 11.925 21960 Z= 0.315 Chirality : 0.042 0.176 2456 Planarity : 0.006 0.257 2696 Dihedral : 7.988 88.196 2460 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.20 % Favored : 92.59 % Rotamer: Outliers : 3.02 % Allowed : 19.14 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1848 helix: 1.61 (0.17), residues: 956 sheet: -0.90 (0.37), residues: 200 loop : -1.57 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.002 0.001 HIS B 379 PHE 0.027 0.001 PHE B 670 TYR 0.012 0.001 TYR D 249 ARG 0.019 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 12) link_NAG-ASN : angle 1.62592 ( 36) hydrogen bonds : bond 0.04327 ( 797) hydrogen bonds : angle 3.72376 ( 2415) SS BOND : bond 0.00529 ( 4) SS BOND : angle 1.94042 ( 8) covalent geometry : bond 0.00292 (16176) covalent geometry : angle 0.59621 (21916) Misc. bond : bond 0.00269 ( 4) *********************** 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 294 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7917 (t80) cc_final: 0.7639 (t80) REVERT: A 252 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8148 (mpp) REVERT: A 255 GLN cc_start: 0.8790 (mt0) cc_final: 0.8541 (mt0) REVERT: A 305 ASN cc_start: 0.7345 (p0) cc_final: 0.6956 (p0) REVERT: A 583 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.4611 (tpt) REVERT: A 590 MET cc_start: 0.6666 (mmt) cc_final: 0.6346 (pp-130) REVERT: A 602 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7739 (tp) REVERT: A 631 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7342 (mt-10) REVERT: A 651 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: B 251 ARG cc_start: 0.8847 (ttt90) cc_final: 0.8610 (ttt90) REVERT: B 252 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8159 (mpp) REVERT: B 305 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6383 (p0) REVERT: B 455 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7690 (p90) REVERT: B 583 MET cc_start: 0.5831 (pmm) cc_final: 0.4888 (tpp) REVERT: B 590 MET cc_start: 0.3917 (mtp) cc_final: 0.3497 (mtm) REVERT: C 252 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: C 305 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6244 (p0) REVERT: C 583 MET cc_start: 0.5893 (pmm) cc_final: 0.4771 (tpt) REVERT: C 590 MET cc_start: 0.4632 (mtp) cc_final: 0.3365 (ptm) REVERT: C 602 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7772 (pp) REVERT: C 603 MET cc_start: 0.7585 (ttp) cc_final: 0.7039 (ttt) REVERT: D 251 ARG cc_start: 0.8847 (ttt90) cc_final: 0.8617 (ttt90) REVERT: D 252 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: D 538 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7866 (t80) REVERT: D 583 MET cc_start: 0.5913 (pmm) cc_final: 0.5037 (tpt) REVERT: D 590 MET cc_start: 0.5793 (ptt) cc_final: 0.4997 (ppp) REVERT: D 603 MET cc_start: 0.7358 (ttp) cc_final: 0.6813 (ttt) REVERT: D 631 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7341 (mt-10) outliers start: 51 outliers final: 23 residues processed: 265 average time/residue: 0.9419 time to fit residues: 285.9410 Evaluate side-chains 269 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET 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 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 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN 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 653 ASN Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 586 LEU 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 166 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 178 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 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 = 0.3889 r_free = 0.3889 target = 0.163696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114583 restraints weight = 18511.704| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.28 r_work: 0.3170 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16196 Z= 0.114 Angle : 0.587 11.086 21960 Z= 0.308 Chirality : 0.041 0.181 2456 Planarity : 0.004 0.042 2696 Dihedral : 7.813 89.072 2460 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.31 % Allowed : 20.26 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1848 helix: 1.66 (0.17), residues: 956 sheet: -0.82 (0.37), residues: 200 loop : -1.57 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.003 0.000 HIS D 379 PHE 0.027 0.001 PHE C 670 TYR 0.010 0.001 TYR D 386 ARG 0.013 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 12) link_NAG-ASN : angle 1.43352 ( 36) hydrogen bonds : bond 0.03930 ( 797) hydrogen bonds : angle 3.65699 ( 2415) SS BOND : bond 0.00352 ( 4) SS BOND : angle 1.50714 ( 8) covalent geometry : bond 0.00238 (16176) covalent geometry : angle 0.58427 (21916) Misc. bond : bond 0.00170 ( 4) *********************** 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: 39 poor density : 254 time to evaluate : 1.717 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: 0.7866 (t80) cc_final: 0.7640 (t80) REVERT: A 252 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8120 (mpp) REVERT: A 305 ASN cc_start: 0.7321 (p0) cc_final: 0.6926 (p0) REVERT: A 343 GLU cc_start: 0.8375 (mp0) cc_final: 0.7892 (mm-30) REVERT: A 583 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4537 (tpt) REVERT: A 590 MET cc_start: 0.6758 (mmt) cc_final: 0.6411 (pp-130) REVERT: A 602 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7679 (tp) REVERT: B 252 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: B 305 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.6559 (p0) REVERT: B 343 GLU cc_start: 0.8346 (mp0) cc_final: 0.7887 (mm-30) REVERT: B 455 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7683 (p90) REVERT: B 583 MET cc_start: 0.5844 (pmm) cc_final: 0.4917 (tpp) REVERT: B 590 MET cc_start: 0.3991 (mtp) cc_final: 0.3559 (mtm) REVERT: C 252 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8095 (mpp) REVERT: C 305 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6348 (p0) REVERT: C 583 MET cc_start: 0.5914 (pmm) cc_final: 0.4791 (tpt) REVERT: C 590 MET cc_start: 0.4387 (mtp) cc_final: 0.3337 (ptm) REVERT: C 603 MET cc_start: 0.7478 (ttp) cc_final: 0.7035 (ttt) REVERT: D 252 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: D 343 GLU cc_start: 0.8372 (mp0) cc_final: 0.8109 (mm-30) REVERT: D 379 HIS cc_start: 0.7364 (m-70) cc_final: 0.7047 (m170) REVERT: D 538 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (t80) REVERT: D 583 MET cc_start: 0.5792 (pmm) cc_final: 0.4973 (tpt) REVERT: D 590 MET cc_start: 0.5774 (ptt) cc_final: 0.5010 (ppp) REVERT: D 603 MET cc_start: 0.7262 (ttp) cc_final: 0.6749 (ttt) outliers start: 39 outliers final: 17 residues processed: 267 average time/residue: 0.9409 time to fit residues: 286.4458 Evaluate side-chains 260 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 677 LEU 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 624 ASP Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN 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 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 0.1980 chunk 71 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 255 GLN B 305 ASN B 543 ASN C 255 GLN C 305 ASN C 543 ASN D 255 GLN D 543 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114087 restraints weight = 18639.918| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.27 r_work: 0.3155 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2550 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= 0.118 Angle : 0.607 14.605 21960 Z= 0.317 Chirality : 0.042 0.185 2456 Planarity : 0.004 0.043 2696 Dihedral : 7.699 89.144 2460 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.13 % Allowed : 21.33 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1848 helix: 1.68 (0.17), residues: 956 sheet: -0.78 (0.37), residues: 200 loop : -1.54 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 414 HIS 0.002 0.000 HIS D 379 PHE 0.028 0.001 PHE A 670 TYR 0.011 0.001 TYR A 249 ARG 0.011 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 12) link_NAG-ASN : angle 1.45123 ( 36) hydrogen bonds : bond 0.03948 ( 797) hydrogen bonds : angle 3.65130 ( 2415) SS BOND : bond 0.00396 ( 4) SS BOND : angle 1.61337 ( 8) covalent geometry : bond 0.00253 (16176) covalent geometry : angle 0.60384 (21916) Misc. bond : bond 0.00114 ( 4) ********************** 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 281 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: A 255 GLN cc_start: 0.8808 (mt0) cc_final: 0.8453 (mt0) REVERT: A 305 ASN cc_start: 0.7276 (p0) cc_final: 0.6867 (p0) REVERT: A 343 GLU cc_start: 0.8390 (mp0) cc_final: 0.7902 (mm-30) REVERT: A 583 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.4563 (tpt) REVERT: A 590 MET cc_start: 0.6580 (mmt) cc_final: 0.6185 (ptm) REVERT: A 602 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7659 (tp) REVERT: B 252 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8094 (mpp) REVERT: B 305 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.6737 (p0) REVERT: B 343 GLU cc_start: 0.8381 (mp0) cc_final: 0.7907 (mm-30) REVERT: B 455 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7702 (p90) REVERT: B 583 MET cc_start: 0.5847 (pmm) cc_final: 0.4926 (tpp) REVERT: B 590 MET cc_start: 0.4035 (mtp) cc_final: 0.3587 (mtm) REVERT: B 602 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7680 (tp) REVERT: B 631 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7212 (mt-10) REVERT: C 252 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8109 (mpp) REVERT: C 305 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6259 (p0) REVERT: C 508 ASN cc_start: 0.8595 (m110) cc_final: 0.8369 (m-40) REVERT: C 583 MET cc_start: 0.5931 (pmm) cc_final: 0.4785 (tpt) REVERT: C 590 MET cc_start: 0.4522 (mtp) cc_final: 0.3430 (ptm) REVERT: C 603 MET cc_start: 0.7448 (ttp) cc_final: 0.7001 (ttt) REVERT: D 252 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8094 (mpp) REVERT: D 343 GLU cc_start: 0.8399 (mp0) cc_final: 0.8134 (mm-30) REVERT: D 379 HIS cc_start: 0.7341 (m-70) cc_final: 0.7079 (m170) REVERT: D 538 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7719 (t80) REVERT: D 583 MET cc_start: 0.5899 (pmm) cc_final: 0.5032 (tpt) REVERT: D 590 MET cc_start: 0.5934 (ptt) cc_final: 0.5106 (ppp) REVERT: D 603 MET cc_start: 0.7241 (ttp) cc_final: 0.6734 (ttt) outliers start: 36 outliers final: 15 residues processed: 257 average time/residue: 0.9693 time to fit residues: 284.8379 Evaluate side-chains 260 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET 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 677 LEU 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 C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 425 ASP 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 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 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 = 0.3868 r_free = 0.3868 target = 0.161906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112392 restraints weight = 18512.609| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.28 r_work: 0.3124 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16196 Z= 0.134 Angle : 0.618 12.751 21960 Z= 0.323 Chirality : 0.042 0.184 2456 Planarity : 0.004 0.045 2696 Dihedral : 7.720 86.578 2460 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.09 % Favored : 92.69 % Rotamer: Outliers : 2.25 % Allowed : 21.39 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1848 helix: 1.69 (0.17), residues: 956 sheet: -0.75 (0.37), residues: 200 loop : -1.52 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 554 HIS 0.001 0.001 HIS B 379 PHE 0.027 0.001 PHE C 670 TYR 0.012 0.001 TYR C 249 ARG 0.011 0.001 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 12) link_NAG-ASN : angle 1.55871 ( 36) hydrogen bonds : bond 0.04240 ( 797) hydrogen bonds : angle 3.68291 ( 2415) SS BOND : bond 0.00497 ( 4) SS BOND : angle 1.89681 ( 8) covalent geometry : bond 0.00303 (16176) covalent geometry : angle 0.61439 (21916) Misc. bond : bond 0.00096 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10626.75 seconds wall clock time: 183 minutes 50.17 seconds (11030.17 seconds total)