Starting phenix.real_space_refine on Sun May 3 12:52:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovt_70912/05_2026/9ovt_70912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovt_70912/05_2026/9ovt_70912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ovt_70912/05_2026/9ovt_70912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovt_70912/05_2026/9ovt_70912.map" model { file = "/net/cci-nas-00/data/ceres_data/9ovt_70912/05_2026/9ovt_70912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovt_70912/05_2026/9ovt_70912.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.956 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 80 5.16 5 Na 3 4.78 5 C 8404 2.51 5 N 2112 2.21 5 O 2396 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13011 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3252 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 399} Chain breaks: 1 Chain: "B" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3194 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3252 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3194 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 396} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' NA': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' NA': 2, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.72, per 1000 atoms: 0.21 Number of scatterers: 13011 At special positions: 0 Unit cell: (132.16, 103.25, 132.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 80 16.00 P 4 15.00 Na 3 11.00 F 12 9.00 O 2396 8.00 N 2112 7.00 C 8404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 500.6 milliseconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 48.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.909A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.837A pdb=" N ALA A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 removed outlier: 3.923A pdb=" N TYR A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.835A pdb=" N GLU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 543 removed outlier: 3.505A pdb=" N MET A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.539A pdb=" N LEU A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 625 removed outlier: 3.893A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.708A pdb=" N PHE A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.561A pdb=" N MET A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.633A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.538A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.525A pdb=" N ASN A 743 " --> pdb=" O ARG A 739 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 758 through 764 Processing helix chain 'A' and resid 789 through 815 removed outlier: 3.521A pdb=" N LEU A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.612A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.554A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.631A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 4.323A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.825A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.622A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.658A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.555A pdb=" N VAL B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.652A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 756 removed outlier: 3.522A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.540A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.910A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 Processing helix chain 'C' and resid 419 through 433 removed outlier: 3.836A pdb=" N ALA C 425 " --> pdb=" O CYS C 421 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 removed outlier: 3.923A pdb=" N TYR C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.835A pdb=" N GLU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 543 removed outlier: 3.504A pdb=" N MET C 523 " --> pdb=" O TYR C 519 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 526 " --> pdb=" O TRP C 522 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 579 removed outlier: 3.539A pdb=" N LEU C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 625 removed outlier: 3.892A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP C 601 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 removed outlier: 3.708A pdb=" N PHE C 655 " --> pdb=" O THR C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 removed outlier: 3.562A pdb=" N MET C 666 " --> pdb=" O VAL C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 removed outlier: 3.633A pdb=" N VAL C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 709 removed outlier: 3.537A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 752 removed outlier: 3.525A pdb=" N ASN C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 747 " --> pdb=" O ASN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 758 Processing helix chain 'C' and resid 758 through 764 Processing helix chain 'C' and resid 789 through 815 removed outlier: 3.521A pdb=" N LEU C 804 " --> pdb=" O GLY C 800 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 807 " --> pdb=" O MET C 803 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.612A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.553A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.630A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 4.323A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 619 " --> pdb=" O SER D 615 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.825A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.622A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.656A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.554A pdb=" N VAL D 690 " --> pdb=" O THR D 686 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.651A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 756 removed outlier: 3.522A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 793 through 817 removed outlier: 3.539A pdb=" N LYS D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 395 removed outlier: 6.494A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 486 Processing sheet with id=AA4, first strand: chain 'A' and resid 699 through 701 removed outlier: 3.974A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.671A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 395 removed outlier: 6.493A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB1, first strand: chain 'C' and resid 485 through 486 Processing sheet with id=AB2, first strand: chain 'C' and resid 699 through 701 removed outlier: 3.975A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 394 through 399 Processing sheet with id=AB4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.671A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1467 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: 1.85 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3992 1.35 - 1.48: 3533 1.48 - 1.61: 5631 1.61 - 1.73: 0 1.73 - 1.86: 138 Bond restraints: 13294 Sorted by residual: bond pdb=" CAT ZK1 B1101 " pdb=" OAA ZK1 B1101 " ideal model delta sigma weight residual 1.214 1.400 -0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" CAU ZK1 A1101 " pdb=" OAB ZK1 A1101 " ideal model delta sigma weight residual 1.215 1.400 -0.185 2.00e-02 2.50e+03 8.54e+01 bond pdb=" CAU ZK1 D1101 " pdb=" OAB ZK1 D1101 " ideal model delta sigma weight residual 1.215 1.400 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" CAT ZK1 A1101 " pdb=" OAA ZK1 A1101 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" CAT ZK1 D1101 " pdb=" OAA ZK1 D1101 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.47e+01 ... (remaining 13289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 16905 2.21 - 4.42: 860 4.42 - 6.63: 131 6.63 - 8.84: 45 8.84 - 11.04: 23 Bond angle restraints: 17964 Sorted by residual: angle pdb=" N VAL C 422 " pdb=" CA VAL C 422 " pdb=" C VAL C 422 " ideal model delta sigma weight residual 111.81 105.59 6.22 8.60e-01 1.35e+00 5.22e+01 angle pdb=" N VAL A 422 " pdb=" CA VAL A 422 " pdb=" C VAL A 422 " ideal model delta sigma weight residual 111.81 105.62 6.19 8.60e-01 1.35e+00 5.19e+01 angle pdb=" C GLN C 638 " pdb=" N THR C 639 " pdb=" CA THR C 639 " ideal model delta sigma weight residual 121.54 132.58 -11.04 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C GLN A 638 " pdb=" N THR A 639 " pdb=" CA THR A 639 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.34e+01 angle pdb=" N SER C 676 " pdb=" CA SER C 676 " pdb=" C SER C 676 " ideal model delta sigma weight residual 110.24 117.31 -7.07 1.30e+00 5.92e-01 2.96e+01 ... (remaining 17959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.26: 7554 19.26 - 38.51: 273 38.51 - 57.77: 60 57.77 - 77.02: 7 77.02 - 96.28: 6 Dihedral angle restraints: 7900 sinusoidal: 3184 harmonic: 4716 Sorted by residual: dihedral pdb=" CA SER D 780 " pdb=" C SER D 780 " pdb=" N LYS D 781 " pdb=" CA LYS D 781 " ideal model delta harmonic sigma weight residual 180.00 121.05 58.95 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA SER B 780 " pdb=" C SER B 780 " pdb=" N LYS B 781 " pdb=" CA LYS B 781 " ideal model delta harmonic sigma weight residual 180.00 121.09 58.91 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA ALA B 786 " pdb=" C ALA B 786 " pdb=" N LEU B 787 " pdb=" CA LEU B 787 " ideal model delta harmonic sigma weight residual 180.00 -142.13 -37.87 0 5.00e+00 4.00e-02 5.74e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1357 0.047 - 0.093: 451 0.093 - 0.140: 115 0.140 - 0.187: 35 0.187 - 0.233: 4 Chirality restraints: 1962 Sorted by residual: chirality pdb=" CA SER D 780 " pdb=" N SER D 780 " pdb=" C SER D 780 " pdb=" CB SER D 780 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA SER B 780 " pdb=" N SER B 780 " pdb=" C SER B 780 " pdb=" CB SER B 780 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASP B 456 " pdb=" N ASP B 456 " pdb=" C ASP B 456 " pdb=" CB ASP B 456 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1959 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 678 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 679 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 678 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO D 679 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 679 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 679 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 669 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C TYR A 669 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR A 669 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A 670 " -0.018 2.00e-02 2.50e+03 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2834 2.77 - 3.31: 11407 3.31 - 3.84: 20859 3.84 - 4.37: 25191 4.37 - 4.90: 42428 Nonbonded interactions: 102719 Sorted by model distance: nonbonded pdb=" OD2 ASP D 779 " pdb=" OG SER D 780 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP B 779 " pdb=" OG SER B 780 " model vdw 2.244 3.040 nonbonded pdb=" OG SER C 543 " pdb=" OE1 GLU D 813 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 543 " pdb=" OE1 GLU B 813 " model vdw 2.290 3.040 nonbonded pdb=" O SER C 533 " pdb=" OG SER C 572 " model vdw 2.321 3.040 ... (remaining 102714 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 387 or resid 390 or resid 393 through 398 or resid 400 thr \ ough 403 or resid 405 through 407 or resid 412 through 414 or resid 416 through \ 422 or resid 424 through 431 or resid 433 or resid 436 or resid 438 or resid 440 \ through 441 or resid 443 through 450 or resid 452 through 454 or resid 456 thro \ ugh 466 or resid 468 through 469 or resid 471 or resid 473 through 545 or resid \ 566 through 581 or resid 583 through 635 or resid 637 through 646 or resid 649 t \ hrough 663 or resid 665 through 670 or resid 672 through 682 or resid 684 throug \ h 685 or resid 688 through 736 or resid 738 or resid 741 through 759 or resid 76 \ 1 through 777 or resid 779 through 795 or resid 797 through 815)) selection = (chain 'B' and (resid 392 or resid 394 or resid 397 through 402 or resid 404 thr \ ough 407 or resid 409 through 411 or resid 416 through 418 or resid 420 through \ 426 or resid 428 through 435 or resid 437 or resid 440 or resid 442 or resid 444 \ through 445 or resid 447 through 454 or resid 456 through 458 or resid 460 thro \ ugh 470 or resid 472 through 473 or resid 475 or resid 477 through 549 or resid \ 570 through 585 or resid 587 through 639 or resid 641 through 650 or resid 653 t \ hrough 667 or resid 669 through 674 or resid 676 through 686 or resid 688 throug \ h 689 or resid 692 through 740 or resid 742 or resid 745 through 763 or resid 76 \ 5 through 781 or resid 783 through 799 or resid 801 through 819)) selection = (chain 'C' and (resid 387 or resid 390 or resid 393 through 398 or resid 400 thr \ ough 403 or resid 405 through 407 or resid 412 through 414 or resid 416 through \ 422 or resid 424 through 431 or resid 433 or resid 436 or resid 438 or resid 440 \ through 441 or resid 443 through 450 or resid 452 through 454 or resid 456 thro \ ugh 466 or resid 468 through 469 or resid 471 or resid 473 through 545 or resid \ 566 through 581 or resid 583 through 635 or resid 637 through 646 or resid 649 t \ hrough 663 or resid 665 through 670 or resid 672 through 682 or resid 684 throug \ h 685 or resid 688 through 736 or resid 738 or resid 741 through 759 or resid 76 \ 1 through 777 or resid 779 through 795 or resid 797 through 815)) selection = (chain 'D' and (resid 392 or resid 394 or resid 397 through 402 or resid 404 thr \ ough 407 or resid 409 through 411 or resid 416 through 418 or resid 420 through \ 426 or resid 428 through 435 or resid 437 or resid 440 or resid 442 or resid 444 \ through 445 or resid 447 through 454 or resid 456 through 458 or resid 460 thro \ ugh 470 or resid 472 through 473 or resid 475 or resid 477 through 549 or resid \ 570 through 585 or resid 587 through 639 or resid 641 through 650 or resid 653 t \ hrough 667 or resid 669 through 674 or resid 676 through 686 or resid 688 throug \ h 689 or resid 692 through 740 or resid 742 or resid 745 through 763 or resid 76 \ 5 through 781 or resid 783 through 799 or resid 801 through 819)) } 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: 7.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.007 0.186 13298 Z= 0.380 Angle : 1.196 11.044 17972 Z= 0.698 Chirality : 0.051 0.233 1962 Planarity : 0.007 0.083 2214 Dihedral : 11.335 96.280 4892 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.70 % Favored : 91.18 % Rotamer: Outliers : 0.29 % Allowed : 4.48 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 7.41 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.49 (0.12), residues: 1632 helix: -4.53 (0.07), residues: 822 sheet: -4.19 (0.29), residues: 168 loop : -3.75 (0.18), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 628 TYR 0.018 0.002 TYR A 465 PHE 0.020 0.002 PHE D 623 TRP 0.017 0.002 TRP D 671 HIS 0.005 0.002 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00723 (13294) covalent geometry : angle 1.19555 (17964) SS BOND : bond 0.00069 ( 4) SS BOND : angle 2.40140 ( 8) hydrogen bonds : bond 0.30754 ( 499) hydrogen bonds : angle 10.55663 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 0.411 Fit side-chains REVERT: A 523 MET cc_start: 0.7135 (mmt) cc_final: 0.6885 (mmt) REVERT: A 541 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7387 (ttt-90) REVERT: A 590 ARG cc_start: 0.6377 (mtm110) cc_final: 0.6099 (ttm110) REVERT: A 631 SER cc_start: 0.7940 (m) cc_final: 0.7415 (p) REVERT: A 634 ASP cc_start: 0.8591 (m-30) cc_final: 0.8143 (m-30) REVERT: A 695 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7576 (mptt) REVERT: B 450 TYR cc_start: 0.7117 (m-80) cc_final: 0.6297 (m-80) REVERT: B 524 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 633 ILE cc_start: 0.8070 (mm) cc_final: 0.7547 (mt) REVERT: C 523 MET cc_start: 0.7138 (mmt) cc_final: 0.6862 (mmt) REVERT: C 542 PHE cc_start: 0.6742 (m-80) cc_final: 0.6351 (m-10) REVERT: C 695 LYS cc_start: 0.8556 (mmtt) cc_final: 0.7525 (mmtt) REVERT: C 756 ASP cc_start: 0.7234 (t0) cc_final: 0.6723 (m-30) REVERT: D 527 MET cc_start: 0.6989 (mmm) cc_final: 0.6758 (ptt) REVERT: D 534 ILE cc_start: 0.8076 (mm) cc_final: 0.7750 (mt) REVERT: D 633 ILE cc_start: 0.8078 (mm) cc_final: 0.7414 (mm) outliers start: 4 outliers final: 2 residues processed: 367 average time/residue: 0.1261 time to fit residues: 64.4248 Evaluate side-chains 224 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 639 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.0050 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 410 GLN A 457 ASN A 583 GLN A 743 ASN B 412 HIS B 726 ASN B 747 ASN C 409 ASN C 410 GLN C 457 ASN C 583 GLN C 743 ASN D 412 HIS D 747 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137638 restraints weight = 15553.509| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.85 r_work: 0.3105 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13298 Z= 0.159 Angle : 0.711 9.922 17972 Z= 0.367 Chirality : 0.044 0.199 1962 Planarity : 0.005 0.061 2214 Dihedral : 7.110 57.445 1878 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.97 % Favored : 91.91 % Rotamer: Outliers : 2.75 % Allowed : 10.91 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.16), residues: 1632 helix: -2.22 (0.14), residues: 834 sheet: -3.67 (0.31), residues: 168 loop : -3.33 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 541 TYR 0.025 0.002 TYR D 405 PHE 0.013 0.001 PHE C 580 TRP 0.013 0.002 TRP B 671 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00362 (13294) covalent geometry : angle 0.71037 (17964) SS BOND : bond 0.01115 ( 4) SS BOND : angle 1.41247 ( 8) hydrogen bonds : bond 0.03968 ( 499) hydrogen bonds : angle 4.65677 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7603 (mmt) cc_final: 0.7334 (mmt) REVERT: A 542 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6782 (t80) REVERT: A 631 SER cc_start: 0.8289 (m) cc_final: 0.8030 (p) REVERT: B 524 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 523 MET cc_start: 0.7505 (mmt) cc_final: 0.7204 (mmt) REVERT: C 756 ASP cc_start: 0.7942 (t0) cc_final: 0.7530 (m-30) REVERT: D 450 TYR cc_start: 0.7934 (m-80) cc_final: 0.7545 (m-80) REVERT: D 527 MET cc_start: 0.7613 (mmm) cc_final: 0.7108 (ptt) REVERT: D 639 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9151 (tp) outliers start: 38 outliers final: 13 residues processed: 270 average time/residue: 0.1119 time to fit residues: 43.5584 Evaluate side-chains 216 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 141 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN B 412 HIS D 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138379 restraints weight = 15742.000| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.82 r_work: 0.3130 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13298 Z= 0.159 Angle : 0.669 9.301 17972 Z= 0.345 Chirality : 0.043 0.178 1962 Planarity : 0.005 0.058 2214 Dihedral : 6.666 58.760 1876 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.95 % Favored : 90.93 % Rotamer: Outliers : 2.46 % Allowed : 13.37 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.19), residues: 1632 helix: -0.90 (0.17), residues: 824 sheet: -3.61 (0.31), residues: 170 loop : -3.07 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 628 TYR 0.023 0.002 TYR D 405 PHE 0.013 0.001 PHE C 580 TRP 0.010 0.001 TRP A 667 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00375 (13294) covalent geometry : angle 0.66856 (17964) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.80133 ( 8) hydrogen bonds : bond 0.03744 ( 499) hydrogen bonds : angle 4.21831 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7720 (mmt) cc_final: 0.7429 (mmt) REVERT: B 524 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7724 (mt-10) REVERT: C 523 MET cc_start: 0.7678 (mmt) cc_final: 0.7367 (mmt) REVERT: C 712 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8305 (ptmm) REVERT: C 756 ASP cc_start: 0.8070 (t0) cc_final: 0.7475 (m-30) REVERT: D 407 MET cc_start: 0.8485 (mtm) cc_final: 0.8207 (mtm) REVERT: D 527 MET cc_start: 0.7627 (mmm) cc_final: 0.7231 (ptt) REVERT: D 571 PHE cc_start: 0.6942 (m-80) cc_final: 0.6703 (m-80) REVERT: D 639 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9056 (tp) outliers start: 34 outliers final: 22 residues processed: 230 average time/residue: 0.1224 time to fit residues: 40.0209 Evaluate side-chains 217 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 712 LYS Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 71 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN D 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140085 restraints weight = 15871.374| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 0.99 r_work: 0.3213 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13298 Z= 0.144 Angle : 0.631 8.192 17972 Z= 0.324 Chirality : 0.043 0.156 1962 Planarity : 0.004 0.055 2214 Dihedral : 6.394 58.461 1876 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.54 % Rotamer: Outliers : 2.17 % Allowed : 15.17 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.20), residues: 1632 helix: -0.23 (0.19), residues: 832 sheet: -3.36 (0.33), residues: 170 loop : -2.94 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 628 TYR 0.022 0.001 TYR D 673 PHE 0.011 0.001 PHE D 608 TRP 0.009 0.001 TRP D 671 HIS 0.007 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00338 (13294) covalent geometry : angle 0.63075 (17964) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.77931 ( 8) hydrogen bonds : bond 0.03399 ( 499) hydrogen bonds : angle 3.92905 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.7995 (p0) cc_final: 0.7777 (p0) REVERT: A 523 MET cc_start: 0.7471 (mmt) cc_final: 0.7191 (mmt) REVERT: B 628 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7388 (mmt180) REVERT: B 704 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8471 (pp) REVERT: C 590 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6741 (mtm180) REVERT: C 633 GLU cc_start: 0.7983 (tp30) cc_final: 0.7763 (tp30) REVERT: C 751 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 756 ASP cc_start: 0.7675 (t0) cc_final: 0.7147 (m-30) REVERT: D 639 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8877 (tp) REVERT: D 704 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8492 (pp) outliers start: 30 outliers final: 18 residues processed: 217 average time/residue: 0.1248 time to fit residues: 37.8902 Evaluate side-chains 201 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 412 HIS B 756 GLN B 764 ASN C 410 GLN C 431 HIS D 412 HIS D 756 GLN D 764 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137377 restraints weight = 15802.025| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.20 r_work: 0.3178 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13298 Z= 0.136 Angle : 0.613 9.730 17972 Z= 0.314 Chirality : 0.042 0.152 1962 Planarity : 0.004 0.055 2214 Dihedral : 6.239 57.723 1876 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.19 % Favored : 90.69 % Rotamer: Outliers : 2.82 % Allowed : 14.23 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.21), residues: 1632 helix: 0.14 (0.19), residues: 832 sheet: -3.11 (0.34), residues: 170 loop : -2.89 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 656 TYR 0.022 0.001 TYR D 405 PHE 0.010 0.001 PHE D 608 TRP 0.009 0.001 TRP D 606 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00320 (13294) covalent geometry : angle 0.61296 (17964) SS BOND : bond 0.00358 ( 4) SS BOND : angle 0.64995 ( 8) hydrogen bonds : bond 0.03321 ( 499) hydrogen bonds : angle 3.79938 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8123 (p0) cc_final: 0.7767 (p0) REVERT: A 523 MET cc_start: 0.7578 (mmt) cc_final: 0.7314 (mmt) REVERT: A 542 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6662 (t80) REVERT: A 590 ARG cc_start: 0.7495 (mtm110) cc_final: 0.6950 (mtm180) REVERT: A 751 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 628 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7478 (mmt180) REVERT: B 704 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8499 (pp) REVERT: C 542 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6821 (t80) REVERT: C 590 ARG cc_start: 0.7313 (mtm110) cc_final: 0.6830 (mtm180) REVERT: C 751 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 756 ASP cc_start: 0.7765 (t0) cc_final: 0.7213 (m-30) REVERT: D 410 LYS cc_start: 0.7821 (tppp) cc_final: 0.7483 (mmtm) REVERT: D 639 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8937 (tp) REVERT: D 704 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8504 (pp) outliers start: 39 outliers final: 20 residues processed: 208 average time/residue: 0.1261 time to fit residues: 36.6082 Evaluate side-chains 206 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 151 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 129 optimal weight: 0.2980 chunk 63 optimal weight: 0.0470 chunk 27 optimal weight: 0.0570 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 756 GLN C 410 GLN D 412 HIS D 756 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135266 restraints weight = 15815.923| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.32 r_work: 0.3178 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13298 Z= 0.112 Angle : 0.594 11.267 17972 Z= 0.304 Chirality : 0.041 0.144 1962 Planarity : 0.004 0.053 2214 Dihedral : 6.071 57.019 1876 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.46 % Favored : 91.42 % Rotamer: Outliers : 2.38 % Allowed : 15.03 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.21), residues: 1632 helix: 0.50 (0.19), residues: 832 sheet: -3.01 (0.35), residues: 170 loop : -2.85 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 656 TYR 0.020 0.001 TYR D 405 PHE 0.010 0.001 PHE B 438 TRP 0.009 0.001 TRP D 606 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00255 (13294) covalent geometry : angle 0.59392 (17964) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.55373 ( 8) hydrogen bonds : bond 0.03135 ( 499) hydrogen bonds : angle 3.67581 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8115 (p0) cc_final: 0.7764 (p0) REVERT: A 523 MET cc_start: 0.7577 (mmt) cc_final: 0.7127 (mmt) REVERT: A 590 ARG cc_start: 0.7477 (mtm110) cc_final: 0.6922 (mtm180) REVERT: A 751 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 756 ASP cc_start: 0.7707 (t0) cc_final: 0.7176 (m-30) REVERT: B 628 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7534 (mmt180) REVERT: B 704 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (pp) REVERT: C 590 ARG cc_start: 0.7348 (mtm110) cc_final: 0.6824 (mtm180) REVERT: C 756 ASP cc_start: 0.7823 (t0) cc_final: 0.7163 (m-30) REVERT: D 410 LYS cc_start: 0.7786 (tppp) cc_final: 0.7501 (mmtm) REVERT: D 628 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7398 (mmt180) REVERT: D 639 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8897 (tp) REVERT: D 704 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (pp) outliers start: 33 outliers final: 21 residues processed: 214 average time/residue: 0.1224 time to fit residues: 36.9448 Evaluate side-chains 204 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 792 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS C 410 GLN C 582 GLN D 412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136620 restraints weight = 15842.250| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.00 r_work: 0.3189 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13298 Z= 0.163 Angle : 0.647 10.977 17972 Z= 0.331 Chirality : 0.043 0.149 1962 Planarity : 0.004 0.051 2214 Dihedral : 6.128 57.605 1876 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 3.11 % Allowed : 14.88 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.21), residues: 1632 helix: 0.55 (0.19), residues: 830 sheet: -2.91 (0.36), residues: 170 loop : -2.83 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.024 0.002 TYR D 405 PHE 0.011 0.001 PHE A 580 TRP 0.010 0.001 TRP D 606 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00388 (13294) covalent geometry : angle 0.64701 (17964) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.69536 ( 8) hydrogen bonds : bond 0.03372 ( 499) hydrogen bonds : angle 3.79726 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.7973 (p0) cc_final: 0.7760 (p0) REVERT: A 523 MET cc_start: 0.7405 (mmt) cc_final: 0.7048 (mmt) REVERT: A 542 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6648 (t80) REVERT: A 590 ARG cc_start: 0.7474 (mtm110) cc_final: 0.6949 (mtm180) REVERT: A 633 GLU cc_start: 0.8173 (tp30) cc_final: 0.7957 (tp30) REVERT: A 657 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8089 (mtm110) REVERT: A 751 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 704 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8528 (pp) REVERT: C 542 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6797 (t80) REVERT: C 590 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6877 (mtm180) REVERT: C 657 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8105 (mtm110) REVERT: C 756 ASP cc_start: 0.7727 (t0) cc_final: 0.7140 (m-30) REVERT: D 410 LYS cc_start: 0.7668 (tppp) cc_final: 0.7370 (mmtm) REVERT: D 628 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7483 (mmt180) REVERT: D 639 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9044 (tp) REVERT: D 704 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8580 (pp) outliers start: 43 outliers final: 27 residues processed: 205 average time/residue: 0.1273 time to fit residues: 36.6748 Evaluate side-chains 208 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 0.0010 chunk 31 optimal weight: 0.0070 chunk 150 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 752 GLN B 412 HIS C 410 GLN C 582 GLN D 412 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136720 restraints weight = 15698.905| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.14 r_work: 0.3186 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13298 Z= 0.126 Angle : 0.614 10.486 17972 Z= 0.314 Chirality : 0.042 0.143 1962 Planarity : 0.004 0.051 2214 Dihedral : 5.964 56.938 1876 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.67 % Allowed : 15.53 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1632 helix: 0.70 (0.19), residues: 838 sheet: -2.78 (0.36), residues: 170 loop : -2.81 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.024 0.001 TYR D 405 PHE 0.021 0.001 PHE D 579 TRP 0.011 0.001 TRP C 574 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00292 (13294) covalent geometry : angle 0.61416 (17964) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.54184 ( 8) hydrogen bonds : bond 0.03145 ( 499) hydrogen bonds : angle 3.66144 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7438 (mmt) cc_final: 0.7067 (mmt) REVERT: A 590 ARG cc_start: 0.7460 (mtm110) cc_final: 0.6951 (mtm180) REVERT: A 633 GLU cc_start: 0.8244 (tp30) cc_final: 0.7967 (tp30) REVERT: A 657 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8137 (mtm110) REVERT: A 751 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 756 ASP cc_start: 0.7629 (t0) cc_final: 0.7080 (m-30) REVERT: B 704 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8477 (pp) REVERT: C 542 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6794 (t80) REVERT: C 590 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6816 (mtm180) REVERT: C 657 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8121 (mtm110) REVERT: C 756 ASP cc_start: 0.7707 (t0) cc_final: 0.7144 (m-30) REVERT: D 410 LYS cc_start: 0.7580 (tppp) cc_final: 0.7327 (mmtm) REVERT: D 628 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7471 (mmt180) REVERT: D 639 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9013 (tp) REVERT: D 704 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8572 (pp) outliers start: 37 outliers final: 26 residues processed: 207 average time/residue: 0.1211 time to fit residues: 35.5171 Evaluate side-chains 207 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.8980 chunk 12 optimal weight: 0.0000 chunk 161 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 32 optimal weight: 0.0270 chunk 133 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 410 GLN A 582 GLN A 752 GLN B 412 HIS C 705 ASN D 412 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.140155 restraints weight = 15775.187| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.10 r_work: 0.3224 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13298 Z= 0.111 Angle : 0.604 10.495 17972 Z= 0.308 Chirality : 0.041 0.140 1962 Planarity : 0.004 0.051 2214 Dihedral : 5.857 56.532 1876 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.31 % Allowed : 16.33 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1632 helix: 0.97 (0.19), residues: 828 sheet: -2.66 (0.37), residues: 168 loop : -2.70 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.021 0.001 TYR D 405 PHE 0.016 0.001 PHE A 537 TRP 0.023 0.001 TRP D 606 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00252 (13294) covalent geometry : angle 0.60416 (17964) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.46076 ( 8) hydrogen bonds : bond 0.03050 ( 499) hydrogen bonds : angle 3.58310 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7434 (mmt) cc_final: 0.7103 (mmt) REVERT: A 542 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6678 (t80) REVERT: A 590 ARG cc_start: 0.7466 (mtm110) cc_final: 0.6975 (mtm180) REVERT: A 657 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8127 (mtm110) REVERT: A 751 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 756 ASP cc_start: 0.7496 (t0) cc_final: 0.6993 (m-30) REVERT: B 704 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8525 (pp) REVERT: C 542 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6822 (t80) REVERT: C 590 ARG cc_start: 0.7346 (mtm110) cc_final: 0.6820 (mtm180) REVERT: C 657 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8144 (mtm110) REVERT: D 410 LYS cc_start: 0.7477 (tppp) cc_final: 0.7262 (mmtm) REVERT: D 639 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8966 (tp) REVERT: D 704 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8571 (pp) outliers start: 32 outliers final: 22 residues processed: 207 average time/residue: 0.1214 time to fit residues: 35.6274 Evaluate side-chains 208 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 102 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 412 HIS C 582 GLN D 412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136621 restraints weight = 15996.095| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.01 r_work: 0.3190 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13298 Z= 0.158 Angle : 0.643 10.759 17972 Z= 0.327 Chirality : 0.043 0.147 1962 Planarity : 0.004 0.050 2214 Dihedral : 5.939 57.129 1876 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.17 % Allowed : 16.62 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.21), residues: 1632 helix: 0.89 (0.19), residues: 828 sheet: -2.76 (0.36), residues: 170 loop : -2.71 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.024 0.002 TYR D 405 PHE 0.015 0.001 PHE C 491 TRP 0.019 0.001 TRP C 574 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00380 (13294) covalent geometry : angle 0.64325 (17964) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.63594 ( 8) hydrogen bonds : bond 0.03269 ( 499) hydrogen bonds : angle 3.69830 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7398 (mmt) cc_final: 0.7100 (mmt) REVERT: A 542 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6637 (t80) REVERT: A 590 ARG cc_start: 0.7457 (mtm110) cc_final: 0.6948 (mtm180) REVERT: A 657 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8118 (mtm110) REVERT: A 751 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 756 ASP cc_start: 0.7616 (t0) cc_final: 0.7037 (m-30) REVERT: B 704 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8599 (pp) REVERT: C 542 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6781 (t80) REVERT: C 590 ARG cc_start: 0.7320 (mtm110) cc_final: 0.6782 (mtm180) REVERT: C 657 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8143 (mtm110) REVERT: C 756 ASP cc_start: 0.7668 (t0) cc_final: 0.7145 (m-30) REVERT: D 410 LYS cc_start: 0.7526 (tppp) cc_final: 0.7303 (mmtm) REVERT: D 704 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8638 (pp) outliers start: 30 outliers final: 21 residues processed: 199 average time/residue: 0.1225 time to fit residues: 34.5068 Evaluate side-chains 203 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 135 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 112 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 752 GLN B 412 HIS D 412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138356 restraints weight = 15806.166| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.15 r_work: 0.3195 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13298 Z= 0.128 Angle : 0.624 11.330 17972 Z= 0.317 Chirality : 0.042 0.142 1962 Planarity : 0.004 0.049 2214 Dihedral : 5.876 56.860 1876 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.95 % Allowed : 16.84 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1632 helix: 1.07 (0.19), residues: 824 sheet: -2.74 (0.36), residues: 170 loop : -2.62 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 541 TYR 0.026 0.001 TYR D 405 PHE 0.015 0.001 PHE A 537 TRP 0.025 0.001 TRP C 574 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00300 (13294) covalent geometry : angle 0.62450 (17964) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.50406 ( 8) hydrogen bonds : bond 0.03132 ( 499) hydrogen bonds : angle 3.61949 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.77 seconds wall clock time: 55 minutes 58.60 seconds (3358.60 seconds total)