Starting phenix.real_space_refine on Tue Dec 31 14:57:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3s_36858/12_2024/8k3s_36858_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3s_36858/12_2024/8k3s_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_36858/12_2024/8k3s_36858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3s_36858/12_2024/8k3s_36858.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3s_36858/12_2024/8k3s_36858_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3s_36858/12_2024/8k3s_36858_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 80 5.16 5 C 10424 2.51 5 N 2444 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.75, per 1000 atoms: 0.62 Number of scatterers: 15761 At special positions: 0 Unit cell: (107.613, 107.613, 96.743, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 80 16.00 P 4 15.00 O 2808 8.00 N 2444 7.00 C 10424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied NAG-ASN " NAG A 802 " - " ASN A 328 " " NAG A 803 " - " ASN A 362 " " NAG A 804 " - " ASN A 375 " " NAG B 802 " - " ASN B 328 " " NAG B 803 " - " ASN B 362 " " NAG B 804 " - " ASN B 375 " " NAG C 802 " - " ASN C 328 " " NAG C 803 " - " ASN C 362 " " NAG C 804 " - " ASN C 375 " " NAG D 802 " - " ASN D 328 " " NAG D 803 " - " ASN D 362 " " NAG D 804 " - " ASN D 375 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.1 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 54.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 215 through 242 Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.638A pdb=" N THR A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 493 removed outlier: 3.613A pdb=" N PHE A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 529 removed outlier: 4.050A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.707A pdb=" N GLN A 537 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.769A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 5.908A pdb=" N THR A 582 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 592 removed outlier: 4.518A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 619 Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.509A pdb=" N ILE A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.879A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 686 removed outlier: 3.635A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.656A pdb=" N THR B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 493 removed outlier: 3.635A pdb=" N PHE B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 529 removed outlier: 4.001A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.655A pdb=" N GLN B 537 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.709A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.944A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 619 Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.872A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 686 removed outlier: 3.522A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.643A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.563A pdb=" N PHE C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 529 removed outlier: 3.994A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 removed outlier: 3.658A pdb=" N GLN C 537 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 538 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.723A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 593 removed outlier: 4.057A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 600 removed outlier: 3.533A pdb=" N PHE C 600 " --> pdb=" O ASP C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 619 Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.870A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 686 removed outlier: 3.507A pdb=" N ILE C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 Processing helix chain 'D' and resid 246 through 259 removed outlier: 3.645A pdb=" N THR D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 493 removed outlier: 3.620A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 529 removed outlier: 4.016A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.711A pdb=" N GLN D 537 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.725A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.538A pdb=" N LEU D 586 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 600 removed outlier: 3.502A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 600 " --> pdb=" O ASP D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 595 through 600' Processing helix chain 'D' and resid 601 through 619 Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.894A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 686 removed outlier: 3.753A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.170A pdb=" N LEU A 316 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL A 428 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL A 318 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 426 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.129A pdb=" N LEU B 316 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 428 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL B 318 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 426 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.129A pdb=" N LEU B 316 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 428 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL B 318 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 426 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.174A pdb=" N LEU C 316 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 428 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL C 318 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE C 426 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.174A pdb=" N LEU C 316 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 428 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL C 318 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE C 426 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AA9, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.128A pdb=" N LEU D 316 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 428 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL D 318 " --> pdb=" O PHE D 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE D 426 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.128A pdb=" N LEU D 316 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 428 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL D 318 " --> pdb=" O PHE D 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE D 426 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 379 through 380 839 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 5.13 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: 0.630 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.810 Find NCS groups from input model: 0.690 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: 0.010 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.990 ------------------------------------------------------------------------------- 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 : 0.004 0.097 16176 Z= 0.237 Angle : 0.757 16.047 21916 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 *********************** 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 : 1.707 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: 1.0779 time to fit residues: 427.3780 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 : 1.872 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 16176 Z= 0.168 Angle : 0.585 7.406 21916 Z= 0.314 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 *********************** 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 : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7921 (t80) cc_final: 0.7662 (t80) REVERT: A 236 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8825 (tp) REVERT: A 305 ASN cc_start: 0.7181 (p0) cc_final: 0.6899 (p0) REVERT: A 602 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7828 (pp) REVERT: A 684 TYR cc_start: 0.5237 (OUTLIER) cc_final: 0.3204 (m-10) REVERT: B 229 LEU cc_start: 0.8542 (mt) cc_final: 0.8265 (mp) REVERT: B 583 MET cc_start: 0.6248 (pmm) cc_final: 0.5518 (tpt) REVERT: B 586 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6670 (OUTLIER) REVERT: C 229 LEU cc_start: 0.8470 (mt) cc_final: 0.8202 (mp) REVERT: C 305 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6718 (p0) REVERT: C 508 ASN cc_start: 0.8533 (m110) cc_final: 0.8264 (m-40) REVERT: C 583 MET cc_start: 0.6062 (pmm) cc_final: 0.5263 (tpt) REVERT: C 590 MET cc_start: 0.4186 (mtp) cc_final: 0.3425 (mmt) REVERT: D 583 MET cc_start: 0.5593 (pmm) cc_final: 0.5101 (tpt) outliers start: 45 outliers final: 10 residues processed: 304 average time/residue: 0.8793 time to fit residues: 307.7602 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 : 1.852 ------------------------------------------------------------------------------- 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 92 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16176 Z= 0.214 Angle : 0.599 7.632 21916 Z= 0.321 Chirality : 0.042 0.182 2456 Planarity : 0.005 0.105 2696 Dihedral : 9.112 89.912 2464 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 3.32 % Allowed : 14.81 % Favored : 81.87 % 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: -0.04 (0.20), residues: 1848 helix: 1.28 (0.17), residues: 972 sheet: -0.92 (0.37), residues: 200 loop : -1.69 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 414 HIS 0.002 0.001 HIS D 498 PHE 0.020 0.001 PHE B 600 TYR 0.020 0.002 TYR D 249 ARG 0.013 0.000 ARG D 440 *********************** 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 319 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7998 (t80) cc_final: 0.7554 (t80) REVERT: A 252 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7144 (mpp) REVERT: A 305 ASN cc_start: 0.7245 (p0) cc_final: 0.6953 (p0) REVERT: A 583 MET cc_start: 0.6099 (pmt) cc_final: 0.4860 (tpt) REVERT: A 651 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: A 684 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.3183 (m-10) REVERT: B 252 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7108 (mpp) REVERT: B 305 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6697 (p0) REVERT: B 583 MET cc_start: 0.6374 (pmm) cc_final: 0.5636 (tpt) REVERT: B 602 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7986 (pp) REVERT: B 651 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: C 252 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7084 (mpp) REVERT: C 305 ASN cc_start: 0.6783 (p0) cc_final: 0.6361 (p0) REVERT: C 583 MET cc_start: 0.6256 (pmm) cc_final: 0.5328 (tpt) REVERT: C 590 MET cc_start: 0.3945 (mtp) cc_final: 0.3388 (mtm) REVERT: C 603 MET cc_start: 0.7361 (ttp) cc_final: 0.7026 (ttt) REVERT: C 651 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: D 252 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7137 (mpp) REVERT: D 305 ASN cc_start: 0.6926 (OUTLIER) cc_final: 0.6688 (p0) REVERT: D 583 MET cc_start: 0.5685 (pmm) cc_final: 0.5176 (tpt) outliers start: 56 outliers final: 15 residues processed: 284 average time/residue: 0.9442 time to fit residues: 308.0174 Evaluate side-chains 263 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 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 266 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 508 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16176 Z= 0.174 Angle : 0.580 7.506 21916 Z= 0.309 Chirality : 0.041 0.161 2456 Planarity : 0.006 0.242 2696 Dihedral : 8.583 83.327 2462 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Rotamer: Outliers : 2.90 % Allowed : 16.71 % Favored : 80.39 % 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: 1.55 (0.17), residues: 944 sheet: -0.87 (0.37), residues: 200 loop : -1.62 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 414 HIS 0.002 0.001 HIS D 498 PHE 0.022 0.001 PHE A 670 TYR 0.015 0.001 TYR C 249 ARG 0.013 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7957 (t80) cc_final: 0.7571 (t80) REVERT: A 305 ASN cc_start: 0.7192 (p0) cc_final: 0.6876 (p0) REVERT: A 583 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.4772 (tpt) REVERT: A 602 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7780 (pp) REVERT: A 631 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6812 (mt-10) REVERT: A 651 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: A 684 TYR cc_start: 0.5182 (OUTLIER) cc_final: 0.3156 (m-10) REVERT: B 251 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7992 (ttt90) REVERT: B 252 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7129 (mpp) REVERT: B 305 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6553 (p0) REVERT: B 583 MET cc_start: 0.6272 (pmm) cc_final: 0.5544 (tpt) REVERT: B 590 MET cc_start: 0.3726 (mtp) cc_final: 0.3228 (mtm) REVERT: B 651 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: C 252 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: C 305 ASN cc_start: 0.6969 (p0) cc_final: 0.6362 (p0) REVERT: C 580 ASN cc_start: 0.6978 (t0) cc_final: 0.6694 (p0) REVERT: C 583 MET cc_start: 0.6246 (pmm) cc_final: 0.5349 (tpt) REVERT: C 590 MET cc_start: 0.3933 (mtp) cc_final: 0.2867 (mmt) REVERT: C 651 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: D 251 ARG cc_start: 0.8219 (ttt90) cc_final: 0.8016 (ttt90) REVERT: D 252 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7109 (mpp) REVERT: D 583 MET cc_start: 0.5457 (pmm) cc_final: 0.4904 (tpt) outliers start: 49 outliers final: 14 residues processed: 283 average time/residue: 0.9465 time to fit residues: 307.0935 Evaluate side-chains 262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE 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 305 ASN Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 255 GLN C 543 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16176 Z= 0.228 Angle : 0.616 8.772 21916 Z= 0.326 Chirality : 0.042 0.155 2456 Planarity : 0.006 0.241 2696 Dihedral : 8.455 84.359 2462 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 3.50 % Allowed : 16.94 % Favored : 79.56 % 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: 0.20 (0.20), residues: 1848 helix: 1.58 (0.17), residues: 944 sheet: -0.94 (0.36), residues: 200 loop : -1.59 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 414 HIS 0.002 0.001 HIS D 379 PHE 0.021 0.001 PHE C 600 TYR 0.018 0.001 TYR A 249 ARG 0.017 0.000 ARG D 440 *********************** 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 319 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7977 (t80) cc_final: 0.7614 (t80) REVERT: A 252 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7166 (mpp) REVERT: A 305 ASN cc_start: 0.7231 (p0) cc_final: 0.6888 (p0) REVERT: A 538 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 583 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.4728 (tpt) REVERT: A 590 MET cc_start: 0.6440 (mmt) cc_final: 0.5825 (ppp) REVERT: A 600 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6812 (p90) REVERT: A 602 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7794 (pp) REVERT: A 631 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 651 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: A 684 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.3181 (m-10) REVERT: B 251 ARG cc_start: 0.8235 (ttt90) cc_final: 0.8009 (ttt90) REVERT: B 252 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7106 (mpp) REVERT: B 305 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6432 (p0) REVERT: B 583 MET cc_start: 0.6254 (pmm) cc_final: 0.5349 (tpt) REVERT: B 590 MET cc_start: 0.3492 (mtp) cc_final: 0.3090 (mtm) REVERT: B 602 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7935 (pp) REVERT: B 651 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: C 251 ARG cc_start: 0.8277 (ttt90) cc_final: 0.8052 (ttt-90) REVERT: C 252 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7168 (mpp) REVERT: C 305 ASN cc_start: 0.6827 (p0) cc_final: 0.6105 (p0) REVERT: C 583 MET cc_start: 0.6421 (pmm) cc_final: 0.5378 (tpt) REVERT: C 590 MET cc_start: 0.3922 (mtp) cc_final: 0.3267 (ptm) REVERT: C 651 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: D 251 ARG cc_start: 0.8247 (ttt90) cc_final: 0.8035 (ttt90) REVERT: D 252 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7131 (mpp) REVERT: D 583 MET cc_start: 0.5645 (pmm) cc_final: 0.4971 (tpt) outliers start: 59 outliers final: 19 residues processed: 281 average time/residue: 0.9559 time to fit residues: 307.6427 Evaluate side-chains 270 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 600 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 482 PHE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 104 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16176 Z= 0.144 Angle : 0.553 6.993 21916 Z= 0.294 Chirality : 0.040 0.139 2456 Planarity : 0.005 0.162 2696 Dihedral : 7.870 87.482 2462 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.67 % Allowed : 18.42 % 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: 0.30 (0.20), residues: 1848 helix: 1.67 (0.17), residues: 952 sheet: -0.84 (0.37), residues: 200 loop : -1.60 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 414 HIS 0.002 0.000 HIS D 498 PHE 0.025 0.001 PHE A 670 TYR 0.011 0.001 TYR C 249 ARG 0.006 0.000 ARG D 440 *********************** 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 303 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7909 (t80) cc_final: 0.7704 (t80) REVERT: A 305 ASN cc_start: 0.7255 (p0) cc_final: 0.6911 (p0) REVERT: A 538 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.8016 (t80) REVERT: A 583 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.4694 (tpt) REVERT: A 590 MET cc_start: 0.6218 (mmt) cc_final: 0.5758 (ptm) REVERT: A 600 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6651 (p90) REVERT: A 602 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7725 (tp) REVERT: B 229 LEU cc_start: 0.8494 (mt) cc_final: 0.8229 (mp) REVERT: B 252 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: B 305 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6510 (p0) REVERT: B 343 GLU cc_start: 0.7694 (mp0) cc_final: 0.7297 (mm-30) REVERT: B 583 MET cc_start: 0.6047 (pmm) cc_final: 0.5205 (tpp) REVERT: B 590 MET cc_start: 0.3732 (mtp) cc_final: 0.3334 (mtm) REVERT: B 602 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 251 ARG cc_start: 0.8165 (ttt90) cc_final: 0.7933 (ttt90) REVERT: C 252 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7022 (mpp) REVERT: C 305 ASN cc_start: 0.6798 (p0) cc_final: 0.6075 (p0) REVERT: C 583 MET cc_start: 0.6130 (pmm) cc_final: 0.5178 (tpt) REVERT: C 590 MET cc_start: 0.3831 (mtp) cc_final: 0.2933 (ptm) REVERT: C 602 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7791 (pp) REVERT: C 651 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: D 252 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7078 (mpp) REVERT: D 343 GLU cc_start: 0.7709 (mp0) cc_final: 0.7304 (mm-30) REVERT: D 538 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7955 (t80) REVERT: D 583 MET cc_start: 0.5531 (pmm) cc_final: 0.4877 (tpt) REVERT: D 600 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6788 (p90) outliers start: 45 outliers final: 12 residues processed: 275 average time/residue: 0.9647 time to fit residues: 305.1790 Evaluate side-chains 257 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 602 ILE 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 651 GLU Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain D residue 252 MET 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 171 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 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 255 GLN A 543 ASN B 255 GLN B 305 ASN B 543 ASN C 543 ASN D 255 GLN D 543 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16176 Z= 0.160 Angle : 0.575 10.671 21916 Z= 0.304 Chirality : 0.041 0.173 2456 Planarity : 0.004 0.120 2696 Dihedral : 7.618 88.939 2460 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Rotamer: Outliers : 2.90 % Allowed : 19.19 % Favored : 77.90 % 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: 0.31 (0.20), residues: 1848 helix: 1.67 (0.17), residues: 956 sheet: -0.83 (0.37), residues: 200 loop : -1.59 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.002 0.001 HIS B 379 PHE 0.022 0.001 PHE B 600 TYR 0.013 0.001 TYR C 249 ARG 0.008 0.000 ARG A 251 *********************** 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 294 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.638 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: 0.7885 (t80) cc_final: 0.7677 (t80) REVERT: A 252 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: A 305 ASN cc_start: 0.7253 (p0) cc_final: 0.6881 (p0) REVERT: A 538 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.8012 (t80) REVERT: A 583 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.4594 (tpt) REVERT: A 602 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7679 (tp) REVERT: B 252 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7034 (mpp) REVERT: B 305 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6301 (p0) REVERT: B 343 GLU cc_start: 0.7714 (mp0) cc_final: 0.7318 (mm-30) REVERT: B 455 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7603 (p90) REVERT: B 583 MET cc_start: 0.6011 (pmm) cc_final: 0.5160 (tpp) REVERT: B 590 MET cc_start: 0.3636 (mtp) cc_final: 0.3253 (mtm) REVERT: B 602 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7874 (pp) REVERT: C 252 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7023 (mpp) REVERT: C 305 ASN cc_start: 0.6824 (p0) cc_final: 0.6077 (p0) REVERT: C 583 MET cc_start: 0.5937 (pmm) cc_final: 0.5024 (tpt) REVERT: C 590 MET cc_start: 0.3871 (mtp) cc_final: 0.2968 (ptm) REVERT: C 602 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7795 (pp) REVERT: D 252 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7121 (mpp) REVERT: D 305 ASN cc_start: 0.6866 (p0) cc_final: 0.6266 (p0) REVERT: D 583 MET cc_start: 0.5578 (pmm) cc_final: 0.5011 (tpt) REVERT: D 600 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6755 (p90) REVERT: D 603 MET cc_start: 0.7051 (ttp) cc_final: 0.6503 (ttt) outliers start: 49 outliers final: 20 residues processed: 262 average time/residue: 0.9795 time to fit residues: 293.3064 Evaluate side-chains 267 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 582 THR 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 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 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 586 LEU Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16176 Z= 0.199 Angle : 0.604 13.664 21916 Z= 0.319 Chirality : 0.042 0.179 2456 Planarity : 0.005 0.126 2696 Dihedral : 7.683 85.649 2460 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.87 % Favored : 92.91 % Rotamer: Outliers : 2.49 % Allowed : 19.96 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.20), residues: 1848 helix: 1.67 (0.17), residues: 948 sheet: -0.87 (0.37), residues: 200 loop : -1.47 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.002 0.001 HIS B 379 PHE 0.027 0.001 PHE A 670 TYR 0.015 0.001 TYR C 249 ARG 0.007 0.000 ARG B 251 *********************** 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 288 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 1.874 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: 0.7906 (t80) cc_final: 0.7694 (t80) REVERT: A 305 ASN cc_start: 0.7244 (p0) cc_final: 0.6890 (p0) REVERT: A 538 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 583 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.4877 (tpt) REVERT: A 602 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 252 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7102 (mpp) REVERT: B 305 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.6316 (p0) REVERT: B 455 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7561 (p90) REVERT: B 583 MET cc_start: 0.5982 (pmm) cc_final: 0.5140 (tpp) REVERT: B 590 MET cc_start: 0.3809 (mtp) cc_final: 0.3398 (mtm) REVERT: C 305 ASN cc_start: 0.6777 (p0) cc_final: 0.5921 (p0) REVERT: C 583 MET cc_start: 0.5921 (pmm) cc_final: 0.4993 (tpt) REVERT: C 590 MET cc_start: 0.3769 (mtp) cc_final: 0.3024 (ptm) REVERT: D 252 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7117 (mpp) REVERT: D 305 ASN cc_start: 0.6867 (p0) cc_final: 0.6214 (p0) REVERT: D 538 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.8031 (t80) REVERT: D 583 MET cc_start: 0.5588 (pmm) cc_final: 0.5022 (tpt) REVERT: D 600 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6770 (p90) REVERT: D 603 MET cc_start: 0.7206 (ttp) cc_final: 0.6585 (ttt) outliers start: 42 outliers final: 21 residues processed: 262 average time/residue: 0.9954 time to fit residues: 296.9797 Evaluate side-chains 267 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU 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 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain 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 600 PHE Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.0070 chunk 155 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16176 Z= 0.153 Angle : 0.590 12.026 21916 Z= 0.311 Chirality : 0.042 0.215 2456 Planarity : 0.004 0.110 2696 Dihedral : 7.432 84.663 2460 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 2.19 % Allowed : 20.38 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1848 helix: 1.87 (0.17), residues: 932 sheet: -0.86 (0.37), residues: 200 loop : -1.53 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 414 HIS 0.002 0.000 HIS D 498 PHE 0.028 0.001 PHE C 670 TYR 0.011 0.001 TYR A 249 ARG 0.008 0.000 ARG D 251 *********************** 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 286 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASN cc_start: 0.7155 (p0) cc_final: 0.6905 (p0) REVERT: A 538 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 583 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5022 (tpt) REVERT: A 602 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7691 (tp) REVERT: B 305 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6503 (p0) REVERT: B 312 GLU cc_start: 0.7534 (pm20) cc_final: 0.7326 (pm20) REVERT: B 343 GLU cc_start: 0.7663 (mp0) cc_final: 0.7240 (mm-30) REVERT: B 455 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.7405 (p90) REVERT: B 583 MET cc_start: 0.5974 (pmm) cc_final: 0.5131 (tpt) REVERT: B 590 MET cc_start: 0.3918 (mtp) cc_final: 0.3509 (mtm) REVERT: B 596 ASP cc_start: 0.5859 (p0) cc_final: 0.5653 (p0) REVERT: C 255 GLN cc_start: 0.8325 (mt0) cc_final: 0.8112 (mt0) REVERT: C 305 ASN cc_start: 0.6868 (p0) cc_final: 0.5992 (p0) REVERT: C 583 MET cc_start: 0.5900 (pmm) cc_final: 0.4984 (tpt) REVERT: C 590 MET cc_start: 0.3627 (mtp) cc_final: 0.2892 (ptm) REVERT: D 305 ASN cc_start: 0.6768 (p0) cc_final: 0.6102 (p0) REVERT: D 312 GLU cc_start: 0.7399 (pm20) cc_final: 0.7154 (pm20) REVERT: D 538 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7944 (t80) REVERT: D 583 MET cc_start: 0.5529 (pmm) cc_final: 0.4955 (tpt) REVERT: D 600 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6233 (t80) outliers start: 37 outliers final: 18 residues processed: 264 average time/residue: 1.0505 time to fit residues: 317.3329 Evaluate side-chains 258 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16176 Z= 0.176 Angle : 0.608 12.750 21916 Z= 0.321 Chirality : 0.042 0.215 2456 Planarity : 0.004 0.117 2696 Dihedral : 7.581 88.690 2460 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.13 % Rotamer: Outliers : 2.01 % Allowed : 20.91 % Favored : 77.07 % 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: 0.47 (0.20), residues: 1848 helix: 1.88 (0.17), residues: 932 sheet: -0.84 (0.37), residues: 200 loop : -1.51 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.001 0.001 HIS C 498 PHE 0.028 0.001 PHE B 670 TYR 0.013 0.001 TYR A 249 ARG 0.010 0.000 ARG C 251 ********************** 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 273 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASN cc_start: 0.7046 (p0) cc_final: 0.6751 (p0) REVERT: A 538 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.8007 (t80) REVERT: A 583 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.4997 (tpt) REVERT: A 602 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7723 (tp) REVERT: B 305 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6651 (p0) REVERT: B 455 TRP cc_start: 0.8226 (OUTLIER) cc_final: 0.7512 (p90) REVERT: B 583 MET cc_start: 0.5980 (pmm) cc_final: 0.5166 (tpp) REVERT: B 590 MET cc_start: 0.3919 (mtp) cc_final: 0.3521 (mtm) REVERT: B 596 ASP cc_start: 0.5852 (p0) cc_final: 0.5642 (p0) REVERT: C 305 ASN cc_start: 0.6982 (p0) cc_final: 0.6013 (p0) REVERT: C 583 MET cc_start: 0.5909 (pmm) cc_final: 0.5002 (tpt) REVERT: C 590 MET cc_start: 0.3504 (mtp) cc_final: 0.2869 (ptm) REVERT: D 305 ASN cc_start: 0.6765 (p0) cc_final: 0.6096 (p0) REVERT: D 538 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7952 (t80) REVERT: D 583 MET cc_start: 0.5424 (pmm) cc_final: 0.4931 (tpt) REVERT: D 600 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6191 (t80) outliers start: 34 outliers final: 20 residues processed: 251 average time/residue: 0.9412 time to fit residues: 270.7396 Evaluate side-chains 256 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 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 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 600 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 155 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 0.0270 chunk 61 optimal weight: 0.0020 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.0052 ------------------------------------------------------------------------------- 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 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113965 restraints weight = 18468.292| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.26 r_work: 0.3157 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16176 Z= 0.176 Angle : 0.604 11.956 21916 Z= 0.320 Chirality : 0.042 0.201 2456 Planarity : 0.004 0.115 2696 Dihedral : 7.581 89.398 2460 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.66 % Favored : 93.18 % Rotamer: Outliers : 2.19 % Allowed : 20.91 % Favored : 76.90 % 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: 0.47 (0.20), residues: 1848 helix: 1.89 (0.17), residues: 932 sheet: -0.86 (0.37), residues: 200 loop : -1.52 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.002 0.001 HIS D 379 PHE 0.027 0.001 PHE C 670 TYR 0.013 0.001 TYR A 249 ARG 0.010 0.000 ARG A 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5477.07 seconds wall clock time: 99 minutes 12.34 seconds (5952.34 seconds total)