Starting phenix.real_space_refine on Fri Jul 3 09:29:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovt_70912/07_2026/9ovt_70912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovt_70912/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ovt_70912/07_2026/9ovt_70912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovt_70912/07_2026/9ovt_70912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ovt_70912/07_2026/9ovt_70912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovt_70912/07_2026/9ovt_70912.map" } 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-dev-6108/lib/python3.11/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, 27 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.09, per 1000 atoms: 0.24 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: 0.82 Conformation dependent library (CDL) restraints added in 465.8 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: 0.32 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: 1.79 Time building geometry restraints manager: 1.14 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: 6.570 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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/Z covalent geometry : bond 0.00723 / 0.38 (13294) covalent geometry : angle 1.19555 / 0.70 (17964) SS BOND : bond 0.00069 / 0.03 ( 4) SS BOND : angle 2.40140 / 1.40 ( 8) hydrogen bonds : bond 0.30754 / 19.99 ( 499) hydrogen bonds : angle 10.55663 / 7.15 ( 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 : 0.487 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: 0.1290 time to fit residues: 65.7930 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 : 0.501 ------------------------------------------------------------------------------- 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... 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 = 0.3911 r_free = 0.3911 target = 0.166326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137877 restraints weight = 15555.178| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.85 r_work: 0.3109 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2837 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= 0.154 Angle : 0.710 9.983 17972 Z= 0.367 Chirality : 0.044 0.192 1962 Planarity : 0.005 0.062 2214 Dihedral : 7.108 57.174 1878 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 2.60 % Allowed : 10.91 % Favored : 86.49 % 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: -4.32 (0.16), residues: 1632 helix: -2.24 (0.14), residues: 836 sheet: -3.67 (0.31), residues: 168 loop : -3.34 (0.20), residues: 628 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 0.014 0.002 TRP B 671 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (13294) covalent geometry : angle 0.70923 / 0.37 (17964) SS BOND : bond 0.00893 / 0.44 ( 4) SS BOND : angle 1.58445 / 0.81 ( 8) hydrogen bonds : bond 0.04049 / 2.66 ( 499) hydrogen bonds : angle 4.68333 / 3.19 ( 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 289 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7578 (mmt) cc_final: 0.7305 (mmt) REVERT: A 542 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6777 (t80) REVERT: A 631 SER cc_start: 0.8297 (m) cc_final: 0.7982 (p) REVERT: B 524 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7768 (mt-10) REVERT: C 523 MET cc_start: 0.7523 (mmt) cc_final: 0.7217 (mmt) REVERT: C 756 ASP cc_start: 0.7945 (t0) cc_final: 0.7517 (m-30) REVERT: D 527 MET cc_start: 0.7602 (mmm) cc_final: 0.7099 (ptt) REVERT: D 639 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9157 (tp) outliers start: 36 outliers final: 12 residues processed: 273 average time/residue: 0.1078 time to fit residues: 42.7756 Evaluate side-chains 219 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 83 optimal weight: 0.9990 chunk 141 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 chunk 42 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 HIS D 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135827 restraints weight = 15748.346| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.82 r_work: 0.3057 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13298 Z= 0.172 Angle : 0.678 9.243 17972 Z= 0.350 Chirality : 0.044 0.178 1962 Planarity : 0.005 0.059 2214 Dihedral : 6.697 58.494 1876 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.31 % Favored : 90.56 % Rotamer: Outliers : 2.67 % Allowed : 13.51 % Favored : 83.82 % 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: -3.00 (0.19), residues: 1632 helix: -0.90 (0.18), residues: 822 sheet: -3.36 (0.35), residues: 146 loop : -3.04 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 628 TYR 0.024 0.002 TYR D 405 PHE 0.014 0.001 PHE C 580 TRP 0.011 0.001 TRP A 667 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (13294) covalent geometry : angle 0.67762 / 0.35 (17964) SS BOND : bond 0.00362 / 0.17 ( 4) SS BOND : angle 0.47881 / 0.23 ( 8) hydrogen bonds : bond 0.03827 / 2.50 ( 499) hydrogen bonds : angle 4.23177 / 2.87 ( 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 247 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: A 523 MET cc_start: 0.7688 (mmt) cc_final: 0.7412 (mmt) REVERT: A 702 SER cc_start: 0.9104 (m) cc_final: 0.8902 (t) REVERT: B 524 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 523 MET cc_start: 0.7718 (mmt) cc_final: 0.7394 (mmt) REVERT: D 407 MET cc_start: 0.8483 (mtm) cc_final: 0.8230 (mtm) REVERT: D 527 MET cc_start: 0.7589 (mmm) cc_final: 0.7196 (ptt) REVERT: D 591 ILE cc_start: 0.7549 (pp) cc_final: 0.7335 (pt) outliers start: 37 outliers final: 24 residues processed: 235 average time/residue: 0.1195 time to fit residues: 39.7918 Evaluate side-chains 219 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 B residue 412 HIS 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 714 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 635 SER 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: 1.9990 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 160 optimal weight: 0.0170 chunk 62 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN 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 = 0.3801 r_free = 0.3801 target = 0.158551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139360 restraints weight = 15809.659| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.13 r_work: 0.3214 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13298 Z= 0.120 Angle : 0.614 8.095 17972 Z= 0.316 Chirality : 0.042 0.180 1962 Planarity : 0.004 0.055 2214 Dihedral : 6.371 59.042 1876 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 2.10 % Allowed : 14.81 % Favored : 83.09 % 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: -2.40 (0.20), residues: 1632 helix: -0.23 (0.19), residues: 832 sheet: -3.37 (0.33), residues: 170 loop : -2.93 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 541 TYR 0.020 0.001 TYR D 405 PHE 0.010 0.001 PHE D 579 TRP 0.008 0.001 TRP D 671 HIS 0.016 0.002 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13294) covalent geometry : angle 0.61357 / 0.32 (17964) SS BOND : bond 0.00281 / 0.14 ( 4) SS BOND : angle 0.64013 / 0.33 ( 8) hydrogen bonds : bond 0.03307 / 2.16 ( 499) hydrogen bonds : angle 3.88314 / 2.62 ( 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 227 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8009 (p0) cc_final: 0.7801 (p0) REVERT: A 523 MET cc_start: 0.7486 (mmt) cc_final: 0.7226 (mmt) REVERT: A 702 SER cc_start: 0.9005 (m) cc_final: 0.8779 (t) REVERT: B 704 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8422 (pp) REVERT: C 523 MET cc_start: 0.7510 (mmt) cc_final: 0.7224 (mmt) REVERT: C 590 ARG cc_start: 0.7355 (mtm110) cc_final: 0.6835 (mtm180) REVERT: C 633 GLU cc_start: 0.7911 (tp30) cc_final: 0.7696 (tp30) REVERT: C 756 ASP cc_start: 0.7819 (t0) cc_final: 0.7148 (m-30) REVERT: D 591 ILE cc_start: 0.7766 (pp) cc_final: 0.7469 (pt) REVERT: D 704 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (pp) REVERT: D 719 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7084 (m-30) outliers start: 29 outliers final: 14 residues processed: 212 average time/residue: 0.1177 time to fit residues: 35.5214 Evaluate side-chains 199 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 626 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 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 D residue 635 SER Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 719 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: 0.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN B 412 HIS B 756 GLN C 410 GLN D 412 HIS D 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137235 restraints weight = 15841.608| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.20 r_work: 0.3164 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13298 Z= 0.140 Angle : 0.610 10.326 17972 Z= 0.314 Chirality : 0.042 0.190 1962 Planarity : 0.004 0.054 2214 Dihedral : 6.247 58.028 1876 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 90.99 % Rotamer: Outliers : 2.38 % Allowed : 14.88 % Favored : 82.73 % 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: 0.12 (0.19), residues: 834 sheet: -3.09 (0.35), residues: 170 loop : -2.86 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 656 TYR 0.022 0.001 TYR D 405 PHE 0.015 0.001 PHE D 579 TRP 0.009 0.001 TRP D 671 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13294) covalent geometry : angle 0.60981 / 0.31 (17964) SS BOND : bond 0.00346 / 0.17 ( 4) SS BOND : angle 0.61166 / 0.31 ( 8) hydrogen bonds : bond 0.03357 / 2.19 ( 499) hydrogen bonds : angle 3.81066 / 2.57 ( 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 217 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8097 (p0) cc_final: 0.7771 (p0) REVERT: A 523 MET cc_start: 0.7543 (mmt) cc_final: 0.7273 (mmt) REVERT: A 590 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6961 (mtm180) REVERT: A 702 SER cc_start: 0.9005 (m) cc_final: 0.8756 (t) REVERT: B 704 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8496 (pp) REVERT: C 542 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6830 (t80) REVERT: C 590 ARG cc_start: 0.7364 (mtm110) cc_final: 0.6877 (mtm180) REVERT: C 751 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 756 ASP cc_start: 0.7854 (t0) cc_final: 0.7086 (m-30) REVERT: D 414 MET cc_start: 0.7493 (pmm) cc_final: 0.7275 (pmm) REVERT: D 591 ILE cc_start: 0.7818 (pp) cc_final: 0.7535 (pt) REVERT: D 704 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8596 (pp) outliers start: 33 outliers final: 21 residues processed: 206 average time/residue: 0.1238 time to fit residues: 36.3851 Evaluate side-chains 202 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 414 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 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 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 592 SER 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: 1.9990 chunk 64 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 27 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A 582 GLN B 412 HIS B 756 GLN B 764 ASN C 410 GLN ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 756 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138553 restraints weight = 15632.851| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 0.96 r_work: 0.3203 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13298 Z= 0.149 Angle : 0.618 9.789 17972 Z= 0.317 Chirality : 0.043 0.198 1962 Planarity : 0.004 0.053 2214 Dihedral : 6.176 57.341 1876 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 90.99 % Rotamer: Outliers : 3.03 % Allowed : 14.31 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.87 (0.21), residues: 1632 helix: 0.31 (0.19), residues: 838 sheet: -2.99 (0.36), residues: 170 loop : -2.90 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 656 TYR 0.023 0.001 TYR D 405 PHE 0.012 0.001 PHE B 438 TRP 0.010 0.001 TRP D 606 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (13294) covalent geometry : angle 0.61796 / 0.32 (17964) SS BOND : bond 0.00360 / 0.18 ( 4) SS BOND : angle 0.61327 / 0.32 ( 8) hydrogen bonds : bond 0.03358 / 2.18 ( 499) hydrogen bonds : angle 3.79297 / 2.56 ( 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 229 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8008 (p0) cc_final: 0.7802 (p0) REVERT: A 523 MET cc_start: 0.7422 (mmt) cc_final: 0.7200 (mmt) REVERT: A 542 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6652 (t80) REVERT: A 590 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6893 (mtm180) REVERT: A 702 SER cc_start: 0.8991 (m) cc_final: 0.8752 (t) REVERT: B 704 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8507 (pp) REVERT: C 542 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6803 (t80) REVERT: C 590 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6840 (mtm180) REVERT: C 751 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7745 (mt-10) REVERT: C 756 ASP cc_start: 0.7825 (t0) cc_final: 0.7023 (m-30) REVERT: D 591 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7519 (pt) REVERT: D 704 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8553 (pp) outliers start: 42 outliers final: 25 residues processed: 214 average time/residue: 0.1168 time to fit residues: 35.6290 Evaluate side-chains 206 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 687 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 414 MET 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 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 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 591 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 136 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN B 412 HIS C 410 GLN C 431 HIS 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 = 0.3782 r_free = 0.3782 target = 0.156027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138931 restraints weight = 15706.784| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 0.96 r_work: 0.3370 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13298 Z= 0.142 Angle : 0.629 11.704 17972 Z= 0.323 Chirality : 0.042 0.188 1962 Planarity : 0.004 0.053 2214 Dihedral : 6.093 57.114 1876 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.52 % Favored : 91.36 % Rotamer: Outliers : 2.67 % Allowed : 15.03 % Favored : 82.30 % 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: -1.61 (0.21), residues: 1632 helix: 0.55 (0.19), residues: 826 sheet: -2.90 (0.36), residues: 170 loop : -2.76 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 541 TYR 0.023 0.001 TYR D 405 PHE 0.020 0.001 PHE D 579 TRP 0.009 0.001 TRP C 574 HIS 0.002 0.001 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13294) covalent geometry : angle 0.62883 / 0.32 (17964) SS BOND : bond 0.00319 / 0.16 ( 4) SS BOND : angle 0.57710 / 0.30 ( 8) hydrogen bonds : bond 0.03267 / 2.13 ( 499) hydrogen bonds : angle 3.73033 / 2.51 ( 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 223 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8088 (p0) cc_final: 0.7851 (p0) REVERT: A 523 MET cc_start: 0.7492 (mmt) cc_final: 0.7143 (mmt) REVERT: A 542 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6628 (t80) REVERT: A 590 ARG cc_start: 0.7490 (mtm110) cc_final: 0.6974 (mtm180) REVERT: A 633 GLU cc_start: 0.8220 (tp30) cc_final: 0.8010 (tp30) REVERT: A 657 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8029 (mtm110) REVERT: A 702 SER cc_start: 0.8953 (m) cc_final: 0.8697 (t) REVERT: B 704 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8508 (pp) REVERT: C 542 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6777 (t80) REVERT: C 590 ARG cc_start: 0.7462 (mtm110) cc_final: 0.6928 (mtm180) REVERT: C 657 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8083 (mtm110) REVERT: C 756 ASP cc_start: 0.7789 (t0) cc_final: 0.7052 (m-30) REVERT: D 591 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7467 (pt) REVERT: D 704 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8580 (pp) outliers start: 37 outliers final: 24 residues processed: 207 average time/residue: 0.1192 time to fit residues: 35.2763 Evaluate side-chains 204 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 725 SER Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 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 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 503 MET Chi-restraints excluded: chain D residue 591 ILE 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: 2.9990 chunk 116 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 119 optimal weight: 0.0010 chunk 31 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A 582 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 = 0.3792 r_free = 0.3792 target = 0.156918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137479 restraints weight = 15635.781| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.17 r_work: 0.3180 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13298 Z= 0.130 Angle : 0.622 10.983 17972 Z= 0.318 Chirality : 0.042 0.184 1962 Planarity : 0.004 0.052 2214 Dihedral : 6.017 56.898 1876 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.67 % Allowed : 15.61 % Favored : 81.72 % 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: -1.44 (0.21), residues: 1632 helix: 0.70 (0.19), residues: 832 sheet: -2.83 (0.36), residues: 170 loop : -2.74 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 541 TYR 0.023 0.001 TYR D 405 PHE 0.018 0.001 PHE A 537 TRP 0.012 0.001 TRP C 574 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13294) covalent geometry : angle 0.62198 / 0.32 (17964) SS BOND : bond 0.00306 / 0.15 ( 4) SS BOND : angle 0.54067 / 0.28 ( 8) hydrogen bonds : bond 0.03177 / 2.07 ( 499) hydrogen bonds : angle 3.67133 / 2.46 ( 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 : 0.409 Fit side-chains revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8113 (p0) cc_final: 0.7879 (p0) REVERT: A 523 MET cc_start: 0.7503 (mmt) cc_final: 0.7121 (mmt) REVERT: A 542 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 590 ARG cc_start: 0.7441 (mtm110) cc_final: 0.6925 (mtm180) REVERT: A 633 GLU cc_start: 0.8349 (tp30) cc_final: 0.8081 (tp30) REVERT: A 635 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8680 (tm) REVERT: A 657 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8126 (mtm110) REVERT: A 702 SER cc_start: 0.9012 (m) cc_final: 0.8776 (t) REVERT: A 756 ASP cc_start: 0.7732 (t0) cc_final: 0.7108 (m-30) REVERT: B 704 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8534 (pp) REVERT: C 542 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6842 (t80) REVERT: C 583 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: C 590 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6828 (mtm180) REVERT: C 657 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8149 (mtm110) REVERT: C 756 ASP cc_start: 0.7901 (t0) cc_final: 0.7076 (m-30) REVERT: D 591 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7434 (pt) REVERT: D 704 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8607 (pp) outliers start: 37 outliers final: 24 residues processed: 207 average time/residue: 0.1200 time to fit residues: 35.2399 Evaluate side-chains 207 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 635 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 414 MET 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 583 GLN 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 591 ILE 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: 0.0770 chunk 161 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 141 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A 582 GLN B 412 HIS C 582 GLN D 412 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138438 restraints weight = 15890.895| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.99 r_work: 0.3207 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13298 Z= 0.133 Angle : 0.621 10.857 17972 Z= 0.317 Chirality : 0.042 0.185 1962 Planarity : 0.004 0.051 2214 Dihedral : 5.958 56.942 1876 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.46 % Allowed : 15.61 % Favored : 81.94 % 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: -1.32 (0.21), residues: 1632 helix: 0.80 (0.19), residues: 832 sheet: -2.83 (0.36), residues: 170 loop : -2.66 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 541 TYR 0.030 0.001 TYR B 732 PHE 0.015 0.001 PHE A 537 TRP 0.015 0.001 TRP A 574 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13294) covalent geometry : angle 0.62135 / 0.32 (17964) SS BOND : bond 0.00288 / 0.14 ( 4) SS BOND : angle 0.54535 / 0.29 ( 8) hydrogen bonds : bond 0.03187 / 2.08 ( 499) hydrogen bonds : angle 3.65765 / 2.45 ( 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 214 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7385 (mmt) cc_final: 0.7038 (mmt) REVERT: A 542 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6624 (t80) REVERT: A 590 ARG cc_start: 0.7394 (mtm110) cc_final: 0.6875 (mtm180) REVERT: A 633 GLU cc_start: 0.8260 (tp30) cc_final: 0.8004 (tp30) REVERT: A 635 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8743 (tm) REVERT: A 657 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8133 (mtm110) REVERT: A 756 ASP cc_start: 0.7619 (t0) cc_final: 0.7017 (m-30) REVERT: B 704 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8566 (pp) REVERT: C 542 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6818 (t80) REVERT: C 590 ARG cc_start: 0.7320 (mtm110) cc_final: 0.6817 (mtm180) REVERT: C 657 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8145 (mtm110) REVERT: C 756 ASP cc_start: 0.7768 (t0) cc_final: 0.7059 (m-30) REVERT: D 591 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7545 (pt) REVERT: D 704 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8647 (pp) outliers start: 34 outliers final: 22 residues processed: 201 average time/residue: 0.1214 time to fit residues: 35.0905 Evaluate side-chains 206 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 542 PHE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 414 MET 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 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 591 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 102 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A 582 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS C 582 GLN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118391 restraints weight = 16292.426| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.12 r_work: 0.3008 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13298 Z= 0.154 Angle : 0.639 11.107 17972 Z= 0.325 Chirality : 0.043 0.234 1962 Planarity : 0.004 0.051 2214 Dihedral : 6.012 57.182 1876 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.46 % Allowed : 15.61 % Favored : 81.94 % 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: -1.32 (0.21), residues: 1632 helix: 0.78 (0.19), residues: 834 sheet: -2.81 (0.36), residues: 170 loop : -2.64 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.027 0.001 TYR A 643 PHE 0.022 0.001 PHE D 579 TRP 0.027 0.002 TRP D 606 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (13294) covalent geometry : angle 0.63870 / 0.33 (17964) SS BOND : bond 0.00307 / 0.15 ( 4) SS BOND : angle 0.61481 / 0.32 ( 8) hydrogen bonds : bond 0.03307 / 2.16 ( 499) hydrogen bonds : angle 3.70837 / 2.49 ( 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 209 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7784 (mmt) cc_final: 0.7577 (mmt) REVERT: A 542 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6711 (t80) REVERT: A 590 ARG cc_start: 0.7515 (mtm110) cc_final: 0.6994 (mtm180) REVERT: A 633 GLU cc_start: 0.8538 (tp30) cc_final: 0.8315 (tp30) REVERT: A 657 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8233 (mtm110) REVERT: B 704 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8683 (pp) REVERT: C 542 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6887 (t80) REVERT: C 590 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6954 (mtm180) REVERT: C 657 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8281 (mtm110) REVERT: C 756 ASP cc_start: 0.8327 (t0) cc_final: 0.7444 (m-30) REVERT: D 591 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7411 (pt) REVERT: D 704 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8744 (pp) outliers start: 34 outliers final: 24 residues processed: 198 average time/residue: 0.1183 time to fit residues: 33.0993 Evaluate side-chains 203 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 725 SER Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 414 MET 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 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 591 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 135 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN A 582 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 = 0.3701 r_free = 0.3701 target = 0.149054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123325 restraints weight = 16165.051| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.76 r_work: 0.3068 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13298 Z= 0.145 Angle : 0.636 12.951 17972 Z= 0.323 Chirality : 0.043 0.222 1962 Planarity : 0.004 0.051 2214 Dihedral : 5.984 57.059 1876 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.24 % Allowed : 15.90 % Favored : 81.86 % 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: -1.21 (0.21), residues: 1632 helix: 0.90 (0.19), residues: 826 sheet: -2.78 (0.36), residues: 170 loop : -2.58 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 541 TYR 0.024 0.001 TYR C 643 PHE 0.014 0.001 PHE A 537 TRP 0.028 0.001 TRP A 574 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (13294) covalent geometry : angle 0.63633 / 0.32 (17964) SS BOND : bond 0.00295 / 0.15 ( 4) SS BOND : angle 0.58089 / 0.31 ( 8) hydrogen bonds : bond 0.03262 / 2.12 ( 499) hydrogen bonds : angle 3.68485 / 2.48 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3298.96 seconds wall clock time: 57 minutes 15.85 seconds (3435.85 seconds total)