Starting phenix.real_space_refine on Sat Jun 14 09:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3s_36858/06_2025/8k3s_36858_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3s_36858/06_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_36858/06_2025/8k3s_36858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3s_36858/06_2025/8k3s_36858.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3s_36858/06_2025/8k3s_36858_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3s_36858/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.28, per 1000 atoms: 0.59 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: 3.69 Conformation dependent library (CDL) restraints added in 1.7 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: 2.08 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: 5.83 Time building geometry restraints manager: 4.38 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: 0.860 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.790 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:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.010 ------------------------------------------------------------------------------- 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 : 1.588 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: 1.0361 time to fit residues: 411.5223 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 : 1.723 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.163714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114132 restraints weight = 18565.286| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.29 r_work: 0.3151 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7934 (t80) cc_final: 0.7660 (t80) REVERT: A 236 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 305 ASN cc_start: 0.7416 (p0) cc_final: 0.7047 (p0) REVERT: A 590 MET cc_start: 0.7057 (mmp) cc_final: 0.6796 (mmt) REVERT: A 602 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 684 TYR cc_start: 0.5221 (OUTLIER) cc_final: 0.3179 (m-10) REVERT: B 229 LEU cc_start: 0.8560 (mt) cc_final: 0.8296 (mp) REVERT: B 583 MET cc_start: 0.6107 (pmm) cc_final: 0.5288 (tpt) REVERT: B 586 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6611 (OUTLIER) REVERT: C 229 LEU cc_start: 0.8498 (mt) cc_final: 0.8245 (mp) REVERT: C 255 GLN cc_start: 0.8748 (mt0) cc_final: 0.8510 (mt0) REVERT: C 305 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6931 (p0) REVERT: C 508 ASN cc_start: 0.8564 (m110) cc_final: 0.8255 (m-40) REVERT: C 583 MET cc_start: 0.5925 (pmm) cc_final: 0.5073 (tpt) REVERT: C 590 MET cc_start: 0.4877 (mtp) cc_final: 0.3822 (mmt) REVERT: D 583 MET cc_start: 0.5748 (pmm) cc_final: 0.5073 (tpt) outliers start: 45 outliers final: 10 residues processed: 304 average time/residue: 0.9162 time to fit residues: 321.4360 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 : 1.678 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.8980 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN B 580 ASN C 543 ASN D 305 ASN D 543 ASN ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106126 restraints weight = 18536.216| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.29 r_work: 0.3039 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16196 Z= 0.244 Angle : 0.715 7.664 21960 Z= 0.378 Chirality : 0.047 0.191 2456 Planarity : 0.006 0.128 2696 Dihedral : 9.429 89.170 2464 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 4.27 % Allowed : 14.63 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.17), residues: 984 sheet: -1.07 (0.36), residues: 200 loop : -1.63 (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 0.022 0.002 PHE B 600 TYR 0.028 0.002 TYR D 249 ARG 0.009 0.001 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 2.33798 ( 36) hydrogen bonds : bond 0.06039 ( 797) hydrogen bonds : angle 4.18225 ( 2415) SS BOND : bond 0.00759 ( 4) SS BOND : angle 3.57704 ( 8) covalent geometry : bond 0.00587 (16176) covalent geometry : angle 0.70626 (21916) Misc. bond : bond 0.00197 ( 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 336 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: A 252 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8202 (mpp) REVERT: A 305 ASN cc_start: 0.7481 (p0) cc_final: 0.7023 (p0) REVERT: A 583 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.4840 (tpt) REVERT: A 631 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 651 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: A 680 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.7004 (mm) REVERT: A 684 TYR cc_start: 0.5178 (OUTLIER) cc_final: 0.3186 (m-10) REVERT: B 252 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8141 (mpp) REVERT: B 305 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6807 (p0) REVERT: B 583 MET cc_start: 0.6265 (pmm) cc_final: 0.5381 (tpt) REVERT: B 602 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8088 (pp) REVERT: B 631 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 651 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: C 252 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: C 255 GLN cc_start: 0.8875 (mt0) cc_final: 0.8666 (mt0) REVERT: C 583 MET cc_start: 0.5979 (pmm) cc_final: 0.4753 (tpt) REVERT: C 590 MET cc_start: 0.4866 (mtp) cc_final: 0.4299 (mtm) REVERT: C 603 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7533 (ttt) REVERT: C 631 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7417 (mt-10) REVERT: C 650 GLU cc_start: 0.8405 (tp30) cc_final: 0.7828 (pt0) REVERT: C 651 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: D 252 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8186 (mpp) REVERT: D 305 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6646 (p0) REVERT: D 538 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7869 (t80) REVERT: D 583 MET cc_start: 0.5844 (pmm) cc_final: 0.5044 (tpt) REVERT: D 602 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (pp) REVERT: D 631 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7474 (mt-10) outliers start: 72 outliers final: 18 residues processed: 295 average time/residue: 0.9236 time to fit residues: 311.3791 Evaluate side-chains 276 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109113 restraints weight = 18377.050| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.25 r_work: 0.3085 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16196 Z= 0.157 Angle : 0.624 7.502 21960 Z= 0.332 Chirality : 0.042 0.163 2456 Planarity : 0.006 0.256 2696 Dihedral : 9.042 89.278 2462 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.33 % Favored : 93.45 % Rotamer: Outliers : 3.38 % Allowed : 16.94 % Favored : 79.68 % 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: -0.06 (0.20), residues: 1848 helix: 1.29 (0.17), residues: 960 sheet: -1.07 (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 0.002 PHE A 670 TYR 0.018 0.001 TYR B 527 ARG 0.025 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 12) link_NAG-ASN : angle 1.84238 ( 36) hydrogen bonds : bond 0.05061 ( 797) hydrogen bonds : angle 3.96814 ( 2415) SS BOND : bond 0.00533 ( 4) SS BOND : angle 2.88286 ( 8) covalent geometry : bond 0.00357 (16176) covalent geometry : angle 0.61784 (21916) Misc. bond : bond 0.00293 ( 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: 57 poor density : 264 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8008 (t80) cc_final: 0.7601 (t80) REVERT: A 252 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8157 (mpp) REVERT: A 305 ASN cc_start: 0.7422 (p0) cc_final: 0.7027 (p0) REVERT: A 583 MET cc_start: 0.6077 (pmt) cc_final: 0.4798 (tpt) REVERT: A 602 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7982 (pp) REVERT: A 631 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 651 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: A 684 TYR cc_start: 0.5108 (OUTLIER) cc_final: 0.3128 (m-10) REVERT: B 251 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8625 (ttt90) REVERT: B 252 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8118 (mpp) REVERT: B 305 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6453 (p0) REVERT: B 583 MET cc_start: 0.6296 (pmm) cc_final: 0.5401 (tpt) REVERT: B 651 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: C 252 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8115 (mpp) REVERT: C 255 GLN cc_start: 0.8771 (mt0) cc_final: 0.8570 (mt0) REVERT: C 583 MET cc_start: 0.6072 (pmm) cc_final: 0.5035 (tpt) REVERT: C 590 MET cc_start: 0.4691 (mtp) cc_final: 0.3295 (mmt) REVERT: C 602 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7754 (pp) REVERT: C 603 MET cc_start: 0.7649 (ttp) cc_final: 0.7247 (ttt) REVERT: C 651 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: D 252 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8117 (mpp) REVERT: D 305 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6800 (p0) REVERT: D 538 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7861 (t80) REVERT: D 583 MET cc_start: 0.5710 (pmm) cc_final: 0.4853 (tpt) outliers start: 57 outliers final: 16 residues processed: 289 average time/residue: 0.9931 time to fit residues: 327.7211 Evaluate side-chains 269 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 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 582 THR Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 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 538 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: 0.9980 chunk 132 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 83 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113228 restraints weight = 18659.251| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.29 r_work: 0.3146 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16196 Z= 0.117 Angle : 0.576 8.384 21960 Z= 0.306 Chirality : 0.040 0.150 2456 Planarity : 0.007 0.282 2696 Dihedral : 8.566 86.024 2462 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.66 % Favored : 93.13 % Rotamer: Outliers : 3.02 % Allowed : 18.07 % Favored : 78.91 % 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: 0.13 (0.20), residues: 1848 helix: 1.56 (0.17), residues: 948 sheet: -0.93 (0.37), residues: 200 loop : -1.69 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 414 HIS 0.003 0.000 HIS D 379 PHE 0.020 0.001 PHE B 600 TYR 0.015 0.001 TYR B 527 ARG 0.006 0.000 ARG D 417 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 12) link_NAG-ASN : angle 1.53455 ( 36) hydrogen bonds : bond 0.04143 ( 797) hydrogen bonds : angle 3.78103 ( 2415) SS BOND : bond 0.00305 ( 4) SS BOND : angle 2.01175 ( 8) covalent geometry : bond 0.00243 (16176) covalent geometry : angle 0.57155 (21916) Misc. bond : bond 0.00249 ( 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 322 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7919 (t80) cc_final: 0.7542 (t80) REVERT: A 255 GLN cc_start: 0.8811 (mt0) cc_final: 0.8505 (mt0) REVERT: A 305 ASN cc_start: 0.7355 (p0) cc_final: 0.6943 (p0) REVERT: A 583 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.4660 (tpt) REVERT: A 590 MET cc_start: 0.6594 (mmt) cc_final: 0.6222 (ptm) REVERT: A 602 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7581 (pp) REVERT: A 631 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7216 (mt-10) REVERT: A 651 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: A 684 TYR cc_start: 0.4990 (OUTLIER) cc_final: 0.3091 (m-10) REVERT: B 251 ARG cc_start: 0.8837 (ttt90) cc_final: 0.8609 (ttt90) REVERT: B 252 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8143 (mpp) REVERT: B 305 ASN cc_start: 0.7140 (OUTLIER) cc_final: 0.6500 (p0) REVERT: B 455 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.7810 (p90) REVERT: B 583 MET cc_start: 0.6127 (pmm) cc_final: 0.5049 (tpt) REVERT: B 590 MET cc_start: 0.3974 (mtp) cc_final: 0.3376 (mtm) REVERT: B 602 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7845 (pp) REVERT: B 651 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: C 252 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8124 (mpp) REVERT: C 255 GLN cc_start: 0.8792 (mt0) cc_final: 0.8554 (mt0) REVERT: C 305 ASN cc_start: 0.6921 (p0) cc_final: 0.6122 (p0) REVERT: C 343 GLU cc_start: 0.8458 (mp0) cc_final: 0.7917 (mm-30) REVERT: C 580 ASN cc_start: 0.6811 (t0) cc_final: 0.6453 (p0) REVERT: C 583 MET cc_start: 0.6119 (pmm) cc_final: 0.4939 (tpt) REVERT: C 590 MET cc_start: 0.4623 (mtp) cc_final: 0.3670 (ptm) REVERT: C 602 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7733 (pp) REVERT: C 603 MET cc_start: 0.7451 (ttp) cc_final: 0.6986 (ttt) REVERT: C 651 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: D 252 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: D 305 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6874 (p0) REVERT: D 343 GLU cc_start: 0.8440 (mp0) cc_final: 0.7901 (mm-30) REVERT: D 583 MET cc_start: 0.5857 (pmm) cc_final: 0.4983 (tpt) REVERT: D 590 MET cc_start: 0.6066 (ptt) cc_final: 0.5216 (ppp) REVERT: D 600 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7341 (p90) REVERT: D 603 MET cc_start: 0.7499 (ttp) cc_final: 0.7024 (ttt) outliers start: 51 outliers final: 15 residues processed: 290 average time/residue: 1.0975 time to fit residues: 364.6520 Evaluate side-chains 271 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 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 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 C residue 252 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 482 PHE 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 305 ASN Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 543 ASN D 255 GLN 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 = 0.3874 r_free = 0.3874 target = 0.162282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113145 restraints weight = 18571.740| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.28 r_work: 0.3140 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2314 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= 0.118 Angle : 0.578 11.031 21960 Z= 0.306 Chirality : 0.041 0.149 2456 Planarity : 0.004 0.126 2696 Dihedral : 8.392 87.996 2462 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.13 % Rotamer: Outliers : 3.08 % Allowed : 18.72 % Favored : 78.20 % 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: 0.21 (0.20), residues: 1848 helix: 1.57 (0.17), residues: 956 sheet: -0.85 (0.37), residues: 200 loop : -1.64 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 414 HIS 0.003 0.001 HIS D 379 PHE 0.024 0.001 PHE D 670 TYR 0.015 0.001 TYR B 527 ARG 0.014 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 12) link_NAG-ASN : angle 1.54218 ( 36) hydrogen bonds : bond 0.04156 ( 797) hydrogen bonds : angle 3.72612 ( 2415) SS BOND : bond 0.00550 ( 4) SS BOND : angle 1.79025 ( 8) covalent geometry : bond 0.00253 (16176) covalent geometry : angle 0.57403 (21916) Misc. bond : bond 0.00182 ( 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 302 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 1.666 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: 0.7930 (t80) cc_final: 0.7653 (t80) REVERT: A 255 GLN cc_start: 0.8809 (mt0) cc_final: 0.8494 (mt0) REVERT: A 305 ASN cc_start: 0.7375 (p0) cc_final: 0.6921 (p0) REVERT: A 583 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.4764 (tpt) REVERT: A 590 MET cc_start: 0.6631 (mmt) cc_final: 0.6375 (pp-130) REVERT: A 631 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 651 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: B 251 ARG cc_start: 0.8791 (ttt90) cc_final: 0.8553 (ttt90) REVERT: B 252 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8146 (mpp) REVERT: B 305 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6446 (p0) REVERT: B 455 TRP cc_start: 0.8411 (OUTLIER) cc_final: 0.7829 (p90) REVERT: B 583 MET cc_start: 0.5911 (pmm) cc_final: 0.4989 (tpp) REVERT: B 590 MET cc_start: 0.3871 (mtp) cc_final: 0.3273 (mtm) REVERT: B 602 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7913 (pp) REVERT: B 651 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: C 252 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: C 255 GLN cc_start: 0.8804 (mt0) cc_final: 0.8560 (mt0) REVERT: C 305 ASN cc_start: 0.6974 (p0) cc_final: 0.6163 (p0) REVERT: C 583 MET cc_start: 0.5946 (pmm) cc_final: 0.4801 (tpt) REVERT: C 590 MET cc_start: 0.4722 (mtp) cc_final: 0.3456 (ptm) REVERT: C 602 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7728 (pp) REVERT: C 603 MET cc_start: 0.7390 (ttp) cc_final: 0.6895 (ttt) REVERT: C 651 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: D 252 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8137 (mpp) REVERT: D 305 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6708 (p0) REVERT: D 379 HIS cc_start: 0.7583 (m-70) cc_final: 0.7381 (m170) REVERT: D 538 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7768 (t80) REVERT: D 583 MET cc_start: 0.5866 (pmm) cc_final: 0.4977 (tpt) REVERT: D 590 MET cc_start: 0.5961 (ptt) cc_final: 0.5099 (ppp) REVERT: D 600 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7222 (p90) REVERT: D 603 MET cc_start: 0.7505 (ttp) cc_final: 0.7021 (ttt) outliers start: 52 outliers final: 19 residues processed: 272 average time/residue: 1.0429 time to fit residues: 324.9507 Evaluate side-chains 275 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR 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 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN 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 600 PHE 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: 3.9990 chunk 138 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.160644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111284 restraints weight = 18547.573| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.27 r_work: 0.3118 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2405 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= 0.137 Angle : 0.595 8.571 21960 Z= 0.314 Chirality : 0.042 0.178 2456 Planarity : 0.004 0.105 2696 Dihedral : 8.322 89.517 2460 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.20 % Favored : 92.59 % Rotamer: Outliers : 3.14 % Allowed : 18.90 % 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: 1.59 (0.17), residues: 956 sheet: -0.90 (0.37), residues: 200 loop : -1.59 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 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 0.013 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 12) link_NAG-ASN : angle 1.65411 ( 36) hydrogen bonds : bond 0.04444 ( 797) hydrogen bonds : angle 3.75395 ( 2415) SS BOND : bond 0.00625 ( 4) SS BOND : angle 2.05806 ( 8) covalent geometry : bond 0.00308 (16176) covalent geometry : angle 0.59078 (21916) Misc. bond : bond 0.00141 ( 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 312 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 1.843 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: 0.7931 (t80) cc_final: 0.7656 (t80) REVERT: A 252 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8200 (mpp) REVERT: A 255 GLN cc_start: 0.8781 (mt0) cc_final: 0.8523 (mt0) REVERT: A 305 ASN cc_start: 0.7381 (p0) cc_final: 0.6910 (p0) REVERT: A 583 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.4646 (tpt) REVERT: A 590 MET cc_start: 0.6621 (mmt) cc_final: 0.6208 (ptm) REVERT: A 602 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7919 (pp) REVERT: A 631 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 651 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 684 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.3101 (m-10) REVERT: B 251 ARG cc_start: 0.8860 (ttt90) cc_final: 0.8624 (ttt90) REVERT: B 252 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: B 305 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6238 (p0) REVERT: B 455 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.7791 (p90) REVERT: B 583 MET cc_start: 0.5897 (pmm) cc_final: 0.4933 (tpp) REVERT: B 590 MET cc_start: 0.3932 (mtp) cc_final: 0.3512 (mtm) REVERT: B 602 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7924 (pp) REVERT: C 252 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8083 (mpp) REVERT: C 305 ASN cc_start: 0.6868 (p0) cc_final: 0.6004 (p0) REVERT: C 583 MET cc_start: 0.5907 (pmm) cc_final: 0.4777 (tpt) REVERT: C 590 MET cc_start: 0.4774 (mtp) cc_final: 0.3401 (ptm) REVERT: C 603 MET cc_start: 0.7554 (ttp) cc_final: 0.6992 (ttt) REVERT: D 251 ARG cc_start: 0.8929 (ttt90) cc_final: 0.8704 (ttt90) REVERT: D 252 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: D 305 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6804 (p0) REVERT: D 343 GLU cc_start: 0.8506 (mp0) cc_final: 0.7986 (mm-30) REVERT: D 538 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7759 (t80) REVERT: D 583 MET cc_start: 0.5926 (pmm) cc_final: 0.5049 (tpt) REVERT: D 590 MET cc_start: 0.5826 (ptt) cc_final: 0.5039 (ppp) REVERT: D 603 MET cc_start: 0.7432 (ttp) cc_final: 0.6932 (ttt) outliers start: 53 outliers final: 25 residues processed: 282 average time/residue: 1.1742 time to fit residues: 379.3920 Evaluate side-chains 279 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 628 THR 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 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 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 305 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 156 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 166 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- 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 543 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108322 restraints weight = 18317.200| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.23 r_work: 0.3073 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16196 Z= 0.193 Angle : 0.664 12.112 21960 Z= 0.347 Chirality : 0.044 0.179 2456 Planarity : 0.005 0.108 2696 Dihedral : 8.604 88.526 2460 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.41 % Favored : 92.37 % Rotamer: Outliers : 2.96 % Allowed : 19.37 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.20), residues: 1848 helix: 1.34 (0.17), residues: 976 sheet: -0.99 (0.37), residues: 200 loop : -1.49 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.009 0.001 HIS D 379 PHE 0.027 0.002 PHE B 670 TYR 0.018 0.002 TYR D 249 ARG 0.013 0.001 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 12) link_NAG-ASN : angle 2.02555 ( 36) hydrogen bonds : bond 0.05317 ( 797) hydrogen bonds : angle 3.88797 ( 2415) SS BOND : bond 0.00801 ( 4) SS BOND : angle 2.74411 ( 8) covalent geometry : bond 0.00457 (16176) covalent geometry : angle 0.65725 (21916) Misc. bond : bond 0.00165 ( 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 297 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 1.908 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 227 TYR cc_start: 0.7987 (t80) cc_final: 0.7615 (t80) REVERT: A 252 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: A 305 ASN cc_start: 0.7344 (p0) cc_final: 0.6891 (p0) REVERT: A 583 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.4522 (tpt) REVERT: A 590 MET cc_start: 0.6651 (mmt) cc_final: 0.6231 (ptm) REVERT: A 602 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8005 (pp) REVERT: A 631 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7128 (mt-10) REVERT: A 651 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: A 684 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.3119 (m-10) REVERT: B 252 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8162 (mpp) REVERT: B 305 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6299 (p0) REVERT: B 455 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7804 (p90) REVERT: B 583 MET cc_start: 0.6031 (pmm) cc_final: 0.4975 (tpp) REVERT: B 590 MET cc_start: 0.4029 (mtp) cc_final: 0.3548 (mtm) REVERT: B 602 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8017 (pp) REVERT: C 252 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8146 (mpp) REVERT: C 305 ASN cc_start: 0.6909 (p0) cc_final: 0.5949 (p0) REVERT: C 508 ASN cc_start: 0.8683 (m110) cc_final: 0.8269 (m-40) REVERT: C 583 MET cc_start: 0.5890 (pmm) cc_final: 0.4731 (tpt) REVERT: C 590 MET cc_start: 0.4804 (mtp) cc_final: 0.3544 (ptm) REVERT: C 603 MET cc_start: 0.7584 (ttp) cc_final: 0.7111 (ttt) REVERT: D 251 ARG cc_start: 0.8986 (ttt90) cc_final: 0.8757 (ttt90) REVERT: D 252 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: D 538 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7845 (t80) REVERT: D 583 MET cc_start: 0.5941 (pmm) cc_final: 0.5038 (tpt) REVERT: D 590 MET cc_start: 0.5879 (ptt) cc_final: 0.5040 (ppp) REVERT: D 603 MET cc_start: 0.7575 (ttp) cc_final: 0.7088 (ttt) outliers start: 50 outliers final: 24 residues processed: 270 average time/residue: 1.0912 time to fit residues: 337.6337 Evaluate side-chains 269 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 500 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 628 THR 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 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 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 538 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 166 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 543 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113556 restraints weight = 18513.969| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.28 r_work: 0.3153 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2519 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 : 0.594 11.232 21960 Z= 0.313 Chirality : 0.041 0.183 2456 Planarity : 0.004 0.089 2696 Dihedral : 8.187 88.453 2460 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.82 % Favored : 93.02 % Rotamer: Outliers : 2.55 % Allowed : 20.08 % Favored : 77.37 % 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: 1.59 (0.17), residues: 956 sheet: -0.85 (0.38), residues: 200 loop : -1.56 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.006 0.001 HIS D 379 PHE 0.023 0.001 PHE B 600 TYR 0.012 0.001 TYR D 227 ARG 0.011 0.000 ARG A 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 12) link_NAG-ASN : angle 1.49565 ( 36) hydrogen bonds : bond 0.04134 ( 797) hydrogen bonds : angle 3.72269 ( 2415) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.65263 ( 8) covalent geometry : bond 0.00251 (16176) covalent geometry : angle 0.59038 (21916) Misc. bond : bond 0.00112 ( 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 295 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7878 (t80) cc_final: 0.7608 (t80) REVERT: A 252 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: A 255 GLN cc_start: 0.8856 (mt0) cc_final: 0.8518 (mt0) REVERT: A 305 ASN cc_start: 0.7318 (p0) cc_final: 0.6900 (p0) REVERT: A 583 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.4579 (tpt) REVERT: A 590 MET cc_start: 0.6840 (mmt) cc_final: 0.6458 (pp-130) REVERT: A 602 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7719 (tp) REVERT: A 631 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 684 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.3162 (m-10) REVERT: B 252 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: B 305 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6401 (p0) REVERT: B 455 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7844 (p90) REVERT: B 583 MET cc_start: 0.5833 (pmm) cc_final: 0.4886 (tpp) REVERT: B 590 MET cc_start: 0.4144 (mtp) cc_final: 0.3682 (mtm) REVERT: B 602 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7741 (tp) REVERT: B 631 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7345 (mt-10) REVERT: C 251 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8684 (ttt90) REVERT: C 252 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: C 305 ASN cc_start: 0.6983 (p0) cc_final: 0.5940 (p0) REVERT: C 343 GLU cc_start: 0.8403 (mp0) cc_final: 0.7882 (mm-30) REVERT: C 583 MET cc_start: 0.5925 (pmm) cc_final: 0.4782 (tpt) REVERT: C 590 MET cc_start: 0.4531 (mtp) cc_final: 0.3364 (ptm) REVERT: C 603 MET cc_start: 0.7572 (ttp) cc_final: 0.7047 (ttt) REVERT: C 631 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7289 (mt-10) REVERT: D 252 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8122 (mpp) REVERT: D 538 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7795 (t80) REVERT: D 583 MET cc_start: 0.6007 (pmm) cc_final: 0.5131 (tpt) REVERT: D 590 MET cc_start: 0.5911 (ptt) cc_final: 0.5104 (ppp) REVERT: D 603 MET cc_start: 0.7455 (ttp) cc_final: 0.6930 (ttt) REVERT: D 631 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7349 (mt-10) outliers start: 43 outliers final: 18 residues processed: 268 average time/residue: 0.9712 time to fit residues: 296.6553 Evaluate side-chains 261 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET 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 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 482 PHE Chi-restraints excluded: chain D residue 538 PHE 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: 5.9990 chunk 71 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 543 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112902 restraints weight = 18666.646| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.29 r_work: 0.3138 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16196 Z= 0.125 Angle : 0.614 14.329 21960 Z= 0.321 Chirality : 0.042 0.188 2456 Planarity : 0.004 0.076 2696 Dihedral : 8.013 89.212 2460 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.87 % Favored : 92.91 % Rotamer: Outliers : 2.13 % Allowed : 21.39 % Favored : 76.48 % 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: 0.29 (0.20), residues: 1848 helix: 1.62 (0.17), residues: 956 sheet: -0.87 (0.37), residues: 200 loop : -1.55 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 414 HIS 0.010 0.001 HIS D 379 PHE 0.027 0.001 PHE A 670 TYR 0.012 0.001 TYR D 227 ARG 0.010 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 12) link_NAG-ASN : angle 1.53543 ( 36) hydrogen bonds : bond 0.04206 ( 797) hydrogen bonds : angle 3.71903 ( 2415) SS BOND : bond 0.00442 ( 4) SS BOND : angle 1.87448 ( 8) covalent geometry : bond 0.00272 (16176) covalent geometry : angle 0.61022 (21916) Misc. bond : bond 0.00108 ( 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 276 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 2.556 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 227 TYR cc_start: 0.7850 (t80) cc_final: 0.7638 (t80) REVERT: A 252 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8133 (mpp) REVERT: A 255 GLN cc_start: 0.8871 (mt0) cc_final: 0.8542 (mt0) REVERT: A 305 ASN cc_start: 0.7296 (p0) cc_final: 0.6854 (p0) REVERT: A 583 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.4518 (tpt) REVERT: A 590 MET cc_start: 0.6713 (mmt) cc_final: 0.6272 (ptm) REVERT: A 631 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7269 (mt-10) REVERT: A 684 TYR cc_start: 0.5088 (OUTLIER) cc_final: 0.3157 (m-10) REVERT: B 252 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8122 (mpp) REVERT: B 305 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6262 (p0) REVERT: B 455 TRP cc_start: 0.8421 (OUTLIER) cc_final: 0.7806 (p90) REVERT: B 583 MET cc_start: 0.5818 (pmm) cc_final: 0.4878 (tpp) REVERT: B 590 MET cc_start: 0.4178 (mtp) cc_final: 0.3716 (mtm) REVERT: B 602 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7739 (tp) REVERT: C 252 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: C 295 MET cc_start: 0.5284 (ppp) cc_final: 0.5057 (ppp) REVERT: C 305 ASN cc_start: 0.7007 (p0) cc_final: 0.5944 (p0) REVERT: C 343 GLU cc_start: 0.8427 (mp0) cc_final: 0.7886 (mm-30) REVERT: C 583 MET cc_start: 0.5886 (pmm) cc_final: 0.4731 (tpt) REVERT: C 590 MET cc_start: 0.4437 (mtp) cc_final: 0.3348 (ptm) REVERT: D 252 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: D 538 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7705 (t80) REVERT: D 583 MET cc_start: 0.5959 (pmm) cc_final: 0.5088 (tpt) REVERT: D 590 MET cc_start: 0.5931 (ptt) cc_final: 0.5108 (ppp) REVERT: D 603 MET cc_start: 0.7424 (ttp) cc_final: 0.6866 (ttt) outliers start: 36 outliers final: 20 residues processed: 254 average time/residue: 1.3390 time to fit residues: 389.1016 Evaluate side-chains 262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET 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 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 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: 7.9990 chunk 35 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 97 optimal weight: 0.1980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 543 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111114 restraints weight = 18487.056| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.27 r_work: 0.3119 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2612 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= 0.144 Angle : 0.630 12.125 21960 Z= 0.330 Chirality : 0.043 0.185 2456 Planarity : 0.004 0.091 2696 Dihedral : 8.008 86.794 2460 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.09 % Favored : 92.69 % Rotamer: Outliers : 2.25 % Allowed : 21.45 % Favored : 76.30 % 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: 0.28 (0.20), residues: 1848 helix: 1.60 (0.17), residues: 956 sheet: -0.90 (0.37), residues: 200 loop : -1.53 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 414 HIS 0.009 0.001 HIS D 379 PHE 0.023 0.001 PHE C 485 TYR 0.014 0.001 TYR B 249 ARG 0.012 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 12) link_NAG-ASN : angle 1.67983 ( 36) hydrogen bonds : bond 0.04548 ( 797) hydrogen bonds : angle 3.75889 ( 2415) SS BOND : bond 0.00570 ( 4) SS BOND : angle 2.21715 ( 8) covalent geometry : bond 0.00326 (16176) covalent geometry : angle 0.62540 (21916) Misc. bond : bond 0.00117 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12087.65 seconds wall clock time: 215 minutes 19.46 seconds (12919.46 seconds total)