Starting phenix.real_space_refine on Thu May 1 07:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y68_33637/05_2025/7y68_33637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y68_33637/05_2025/7y68_33637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y68_33637/05_2025/7y68_33637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y68_33637/05_2025/7y68_33637.map" model { file = "/net/cci-nas-00/data/ceres_data/7y68_33637/05_2025/7y68_33637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y68_33637/05_2025/7y68_33637.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.073 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 62 5.16 5 C 6642 2.51 5 N 1668 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5019 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 627} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 5019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5019 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 627} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.24, per 1000 atoms: 0.61 Number of scatterers: 10264 At special positions: 0 Unit cell: (102.837, 81.1875, 133.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 62 16.00 O 1890 8.00 N 1668 7.00 C 6642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 27 " " NAG A 903 " - " ASN A 141 " " NAG A 904 " - " ASN A 123 " " NAG A 905 " - " ASN A 60 " " NAG B 902 " - " ASN B 27 " " NAG B 903 " - " ASN B 141 " " NAG B 904 " - " ASN B 123 " " NAG B 905 " - " ASN B 60 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN B 54 " " NAG F 1 " - " ASN B 165 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 568 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 568 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 46.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.775A pdb=" N VAL A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 479 removed outlier: 3.558A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 4.724A pdb=" N VAL A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.782A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.535A pdb=" N ALA A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.333A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 581' Processing helix chain 'A' and resid 582 through 599 removed outlier: 3.966A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 626 removed outlier: 3.824A pdb=" N TYR A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 614 " --> pdb=" O TYR A 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.722A pdb=" N ALA A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.638A pdb=" N LEU A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 704 " --> pdb=" O TRP A 700 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 709 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.602A pdb=" N ALA A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 769 removed outlier: 3.512A pdb=" N VAL A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 755 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 removed outlier: 3.635A pdb=" N GLU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 817 removed outlier: 3.711A pdb=" N SER A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 813 " --> pdb=" O GLY A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 290 through 319 removed outlier: 3.775A pdb=" N VAL B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 479 removed outlier: 3.558A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 4.725A pdb=" N VAL B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.782A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.536A pdb=" N ALA B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 removed outlier: 4.333A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 576 through 581' Processing helix chain 'B' and resid 582 through 599 removed outlier: 3.966A pdb=" N ILE B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 594 " --> pdb=" O CYS B 590 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 626 removed outlier: 3.824A pdb=" N TYR B 607 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 652 removed outlier: 3.723A pdb=" N ALA B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.638A pdb=" N LEU B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B 693 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 704 " --> pdb=" O TRP B 700 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.602A pdb=" N ALA B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 769 removed outlier: 3.512A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 removed outlier: 3.635A pdb=" N GLU B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 817 removed outlier: 3.711A pdb=" N SER B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 813 " --> pdb=" O GLY B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32 removed outlier: 6.635A pdb=" N ASN A 27 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE A 50 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 29 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR A 52 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 31 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASN A 54 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU A 47 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 136 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.925A pdb=" N GLY A 64 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.871A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.645A pdb=" N SER A 198 " --> pdb=" O MET A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 32 removed outlier: 6.634A pdb=" N ASN B 27 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE B 50 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER B 29 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 52 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ASN B 54 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU B 47 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR B 136 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.925A pdb=" N GLY B 64 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.870A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166 Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.646A pdb=" N SER B 198 " --> pdb=" O MET B 225 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1476 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: 3.22 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1632 1.30 - 1.43: 2862 1.43 - 1.56: 5902 1.56 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 10490 Sorted by residual: bond pdb=" N ARG A 100 " pdb=" CA ARG A 100 " ideal model delta sigma weight residual 1.455 1.384 0.070 1.25e-02 6.40e+03 3.18e+01 bond pdb=" C ARG B 100 " pdb=" N GLY B 101 " ideal model delta sigma weight residual 1.325 1.265 0.060 1.27e-02 6.20e+03 2.24e+01 bond pdb=" C ARG B 100 " pdb=" O ARG B 100 " ideal model delta sigma weight residual 1.234 1.176 0.057 1.25e-02 6.40e+03 2.10e+01 bond pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 1.524 1.466 0.059 1.31e-02 5.83e+03 2.02e+01 bond pdb=" C ARG A 100 " pdb=" N GLY A 101 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.46e-02 4.69e+03 2.01e+01 ... (remaining 10485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 14081 2.41 - 4.82: 179 4.82 - 7.23: 23 7.23 - 9.64: 4 9.64 - 12.05: 1 Bond angle restraints: 14288 Sorted by residual: angle pdb=" C LEU A 99 " pdb=" N ARG A 100 " pdb=" CA ARG A 100 " ideal model delta sigma weight residual 123.05 111.00 12.05 1.79e+00 3.12e-01 4.53e+01 angle pdb=" N ARG A 100 " pdb=" CA ARG A 100 " pdb=" C ARG A 100 " ideal model delta sigma weight residual 110.14 118.11 -7.97 1.47e+00 4.63e-01 2.94e+01 angle pdb=" C LEU B 99 " pdb=" N ARG B 100 " pdb=" CA ARG B 100 " ideal model delta sigma weight residual 122.74 114.23 8.51 1.82e+00 3.02e-01 2.19e+01 angle pdb=" N ARG B 100 " pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 110.42 117.50 -7.08 1.55e+00 4.16e-01 2.09e+01 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 117.83 -8.02 2.21e+00 2.05e-01 1.32e+01 ... (remaining 14283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 5760 21.71 - 43.43: 407 43.43 - 65.14: 97 65.14 - 86.86: 38 86.86 - 108.57: 92 Dihedral angle restraints: 6394 sinusoidal: 2570 harmonic: 3824 Sorted by residual: dihedral pdb=" CA PHE A 195 " pdb=" C PHE A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 126.21 53.79 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta harmonic sigma weight residual 180.00 126.29 53.71 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CB CYS B 197 " pdb=" SG CYS B 197 " pdb=" SG CYS B 256 " pdb=" CB CYS B 256 " ideal model delta sinusoidal sigma weight residual 93.00 162.11 -69.11 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 6391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1686 0.128 - 0.255: 20 0.255 - 0.382: 6 0.382 - 0.510: 1 0.510 - 0.637: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA ARG A 100 " pdb=" N ARG A 100 " pdb=" C ARG A 100 " pdb=" CB ARG A 100 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ARG B 100 " pdb=" N ARG B 100 " pdb=" C ARG B 100 " pdb=" CB ARG B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 27 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1711 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.062 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO B 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 462 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 463 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.030 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1421 2.75 - 3.29: 10036 3.29 - 3.83: 16595 3.83 - 4.36: 20204 4.36 - 4.90: 34093 Nonbonded interactions: 82349 Sorted by model distance: nonbonded pdb=" OD1 ASN A 506 " pdb=" OG SER A 564 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN B 506 " pdb=" OG SER B 564 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A 702 " pdb=" OH TYR A 717 " model vdw 2.220 3.040 nonbonded pdb=" O LEU B 702 " pdb=" OH TYR B 717 " model vdw 2.220 3.040 nonbonded pdb=" NE2 GLN A 472 " pdb=" O VAL A 569 " model vdw 2.227 3.120 ... (remaining 82344 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.860 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 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:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.005 0.070 10520 Z= 0.257 Angle : 0.728 12.054 14352 Z= 0.386 Chirality : 0.052 0.637 1714 Planarity : 0.005 0.093 1790 Dihedral : 22.415 108.571 3894 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1288 helix: -0.90 (0.23), residues: 482 sheet: 0.12 (0.30), residues: 284 loop : -1.81 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 634 HIS 0.005 0.001 HIS A 492 PHE 0.013 0.002 PHE A 764 TYR 0.020 0.002 TYR A 729 ARG 0.007 0.001 ARG B 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 12) link_NAG-ASN : angle 3.91198 ( 36) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 1.76287 ( 12) hydrogen bonds : bond 0.24140 ( 510) hydrogen bonds : angle 8.04533 ( 1476) metal coordination : bond 0.00265 ( 6) SS BOND : bond 0.00126 ( 8) SS BOND : angle 0.91541 ( 16) covalent geometry : bond 0.00506 (10490) covalent geometry : angle 0.69983 (14288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 HIS cc_start: 0.7782 (m90) cc_final: 0.7581 (m90) REVERT: A 551 TYR cc_start: 0.8090 (m-10) cc_final: 0.7871 (m-80) REVERT: A 595 TYR cc_start: 0.7816 (t80) cc_final: 0.7380 (t80) REVERT: B 551 TYR cc_start: 0.8083 (m-10) cc_final: 0.7868 (m-80) REVERT: B 595 TYR cc_start: 0.7813 (t80) cc_final: 0.7377 (t80) outliers start: 1 outliers final: 2 residues processed: 134 average time/residue: 0.8867 time to fit residues: 131.6169 Evaluate side-chains 101 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 709 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 712 ASN B 476 ASN B 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088520 restraints weight = 16074.494| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.91 r_work: 0.3034 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10520 Z= 0.219 Angle : 0.745 8.067 14352 Z= 0.366 Chirality : 0.051 0.292 1714 Planarity : 0.005 0.091 1790 Dihedral : 19.091 78.632 1734 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.90 % Allowed : 9.77 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1288 helix: -0.47 (0.21), residues: 540 sheet: 0.23 (0.30), residues: 278 loop : -2.26 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.004 0.001 HIS A 492 PHE 0.022 0.002 PHE A 582 TYR 0.018 0.002 TYR A 717 ARG 0.006 0.001 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 3.22943 ( 36) link_BETA1-4 : bond 0.00199 ( 4) link_BETA1-4 : angle 1.36520 ( 12) hydrogen bonds : bond 0.05981 ( 510) hydrogen bonds : angle 5.20802 ( 1476) metal coordination : bond 0.00525 ( 6) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.06795 ( 16) covalent geometry : bond 0.00503 (10490) covalent geometry : angle 0.72719 (14288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8425 (m-30) cc_final: 0.8176 (m-30) REVERT: A 94 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7487 (pp30) REVERT: A 546 HIS cc_start: 0.7927 (m90) cc_final: 0.7603 (m90) REVERT: A 551 TYR cc_start: 0.8162 (m-80) cc_final: 0.7952 (m-80) REVERT: A 595 TYR cc_start: 0.7760 (t80) cc_final: 0.7126 (t80) REVERT: B 41 ASP cc_start: 0.8423 (m-30) cc_final: 0.8171 (m-30) REVERT: B 94 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7479 (pp30) REVERT: B 551 TYR cc_start: 0.8150 (m-80) cc_final: 0.7895 (m-80) REVERT: B 595 TYR cc_start: 0.7761 (t80) cc_final: 0.7125 (t80) outliers start: 20 outliers final: 4 residues processed: 124 average time/residue: 1.0620 time to fit residues: 150.5323 Evaluate side-chains 106 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 476 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.142491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095092 restraints weight = 16681.290| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.95 r_work: 0.3159 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10520 Z= 0.156 Angle : 0.660 9.909 14352 Z= 0.317 Chirality : 0.048 0.306 1714 Planarity : 0.004 0.075 1790 Dihedral : 10.134 59.441 1728 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.18 % Allowed : 13.00 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1288 helix: 0.00 (0.22), residues: 548 sheet: 0.19 (0.29), residues: 290 loop : -2.12 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.003 0.001 HIS A 492 PHE 0.013 0.001 PHE A 730 TYR 0.013 0.001 TYR A 584 ARG 0.004 0.001 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 12) link_NAG-ASN : angle 2.72128 ( 36) link_BETA1-4 : bond 0.00662 ( 4) link_BETA1-4 : angle 1.16259 ( 12) hydrogen bonds : bond 0.04551 ( 510) hydrogen bonds : angle 4.57546 ( 1476) metal coordination : bond 0.00329 ( 6) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.86581 ( 16) covalent geometry : bond 0.00356 (10490) covalent geometry : angle 0.64577 (14288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8414 (m-30) cc_final: 0.8134 (m-30) REVERT: A 94 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: A 122 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8685 (tmmt) REVERT: A 546 HIS cc_start: 0.8054 (m90) cc_final: 0.7700 (m90) REVERT: A 551 TYR cc_start: 0.8296 (m-80) cc_final: 0.8054 (m-80) REVERT: A 595 TYR cc_start: 0.7809 (t80) cc_final: 0.7074 (t80) REVERT: B 41 ASP cc_start: 0.8415 (m-30) cc_final: 0.8152 (m-30) REVERT: B 94 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: B 122 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8690 (tmmt) REVERT: B 551 TYR cc_start: 0.8292 (m-80) cc_final: 0.8049 (m-80) outliers start: 23 outliers final: 3 residues processed: 130 average time/residue: 0.7722 time to fit residues: 113.3461 Evaluate side-chains 111 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.141757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093973 restraints weight = 16511.600| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.94 r_work: 0.3150 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10520 Z= 0.186 Angle : 0.632 10.078 14352 Z= 0.312 Chirality : 0.047 0.283 1714 Planarity : 0.004 0.079 1790 Dihedral : 8.076 58.380 1728 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.04 % Allowed : 14.61 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1288 helix: 0.30 (0.22), residues: 548 sheet: 0.29 (0.29), residues: 290 loop : -2.08 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS B 492 PHE 0.013 0.001 PHE A 730 TYR 0.013 0.001 TYR A 173 ARG 0.006 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 12) link_NAG-ASN : angle 2.59168 ( 36) link_BETA1-4 : bond 0.00440 ( 4) link_BETA1-4 : angle 1.61704 ( 12) hydrogen bonds : bond 0.04375 ( 510) hydrogen bonds : angle 4.49180 ( 1476) metal coordination : bond 0.00325 ( 6) SS BOND : bond 0.00138 ( 8) SS BOND : angle 1.01444 ( 16) covalent geometry : bond 0.00438 (10490) covalent geometry : angle 0.61751 (14288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8408 (m-30) cc_final: 0.8160 (m-30) REVERT: A 94 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: A 122 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8523 (tmmt) REVERT: A 546 HIS cc_start: 0.8079 (m90) cc_final: 0.7710 (m90) REVERT: A 551 TYR cc_start: 0.8338 (m-80) cc_final: 0.8067 (m-80) REVERT: A 562 LEU cc_start: 0.8666 (mt) cc_final: 0.8398 (mm) REVERT: B 41 ASP cc_start: 0.8413 (m-30) cc_final: 0.8145 (m-30) REVERT: B 94 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: B 551 TYR cc_start: 0.8337 (m-80) cc_final: 0.8069 (m-80) outliers start: 32 outliers final: 12 residues processed: 129 average time/residue: 0.9831 time to fit residues: 140.6634 Evaluate side-chains 117 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.142906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095023 restraints weight = 16528.307| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.99 r_work: 0.3121 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10520 Z= 0.212 Angle : 0.626 9.201 14352 Z= 0.314 Chirality : 0.047 0.275 1714 Planarity : 0.004 0.070 1790 Dihedral : 7.408 53.165 1728 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.04 % Allowed : 15.65 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1288 helix: 0.41 (0.22), residues: 554 sheet: 0.31 (0.29), residues: 290 loop : -2.05 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 317 HIS 0.004 0.001 HIS A 492 PHE 0.013 0.001 PHE A 730 TYR 0.014 0.002 TYR A 173 ARG 0.004 0.001 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 12) link_NAG-ASN : angle 2.45175 ( 36) link_BETA1-4 : bond 0.00370 ( 4) link_BETA1-4 : angle 1.57503 ( 12) hydrogen bonds : bond 0.04385 ( 510) hydrogen bonds : angle 4.42932 ( 1476) metal coordination : bond 0.00406 ( 6) SS BOND : bond 0.00182 ( 8) SS BOND : angle 1.00974 ( 16) covalent geometry : bond 0.00503 (10490) covalent geometry : angle 0.61219 (14288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8541 (m-30) cc_final: 0.8226 (m-30) REVERT: A 94 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: A 153 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7542 (p0) REVERT: A 546 HIS cc_start: 0.8138 (m90) cc_final: 0.7764 (m90) REVERT: A 551 TYR cc_start: 0.8532 (m-80) cc_final: 0.8253 (m-80) REVERT: A 562 LEU cc_start: 0.8693 (mt) cc_final: 0.8430 (mm) REVERT: A 592 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 41 ASP cc_start: 0.8471 (m-30) cc_final: 0.8185 (m-30) REVERT: B 94 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: B 153 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7543 (p0) REVERT: B 551 TYR cc_start: 0.8539 (m-80) cc_final: 0.8255 (m-80) REVERT: B 562 LEU cc_start: 0.8710 (mt) cc_final: 0.8452 (mm) REVERT: B 592 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7907 (tp) outliers start: 32 outliers final: 10 residues processed: 124 average time/residue: 0.8147 time to fit residues: 113.8779 Evaluate side-chains 125 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.144059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096396 restraints weight = 16536.777| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.00 r_work: 0.3157 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10520 Z= 0.150 Angle : 0.574 8.582 14352 Z= 0.288 Chirality : 0.045 0.251 1714 Planarity : 0.004 0.072 1790 Dihedral : 6.813 46.699 1728 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.66 % Allowed : 17.36 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1288 helix: 0.61 (0.22), residues: 566 sheet: 0.35 (0.29), residues: 290 loop : -1.91 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 317 HIS 0.004 0.001 HIS B 492 PHE 0.012 0.001 PHE A 730 TYR 0.012 0.001 TYR B 584 ARG 0.003 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 2.16558 ( 36) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 1.34506 ( 12) hydrogen bonds : bond 0.04026 ( 510) hydrogen bonds : angle 4.28880 ( 1476) metal coordination : bond 0.00235 ( 6) SS BOND : bond 0.00135 ( 8) SS BOND : angle 0.91067 ( 16) covalent geometry : bond 0.00349 (10490) covalent geometry : angle 0.56316 (14288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8442 (m-30) cc_final: 0.8172 (m-30) REVERT: A 94 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: A 122 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8526 (tmmt) REVERT: A 546 HIS cc_start: 0.8080 (m90) cc_final: 0.7687 (m90) REVERT: A 551 TYR cc_start: 0.8471 (m-80) cc_final: 0.8201 (m-80) REVERT: A 562 LEU cc_start: 0.8689 (mt) cc_final: 0.8463 (mm) REVERT: A 592 LEU cc_start: 0.8375 (mm) cc_final: 0.7958 (tp) REVERT: B 41 ASP cc_start: 0.8440 (m-30) cc_final: 0.8160 (m-30) REVERT: B 94 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: B 122 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8530 (tmmt) REVERT: B 551 TYR cc_start: 0.8488 (m-80) cc_final: 0.8205 (m-80) REVERT: B 562 LEU cc_start: 0.8681 (mt) cc_final: 0.8414 (mm) REVERT: B 592 LEU cc_start: 0.8270 (mm) cc_final: 0.7867 (tp) outliers start: 28 outliers final: 8 residues processed: 132 average time/residue: 0.7386 time to fit residues: 110.1401 Evaluate side-chains 118 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.139552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090119 restraints weight = 16383.228| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.00 r_work: 0.3078 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10520 Z= 0.161 Angle : 0.582 8.786 14352 Z= 0.294 Chirality : 0.045 0.240 1714 Planarity : 0.004 0.067 1790 Dihedral : 6.530 46.609 1728 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.18 % Allowed : 19.07 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1288 helix: 0.82 (0.23), residues: 556 sheet: 0.36 (0.29), residues: 290 loop : -1.76 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 317 HIS 0.004 0.001 HIS B 492 PHE 0.013 0.001 PHE A 576 TYR 0.013 0.001 TYR B 173 ARG 0.002 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 2.04887 ( 36) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.26496 ( 12) hydrogen bonds : bond 0.04000 ( 510) hydrogen bonds : angle 4.26370 ( 1476) metal coordination : bond 0.00277 ( 6) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.92155 ( 16) covalent geometry : bond 0.00380 (10490) covalent geometry : angle 0.57169 (14288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8352 (m-30) cc_final: 0.8073 (m-30) REVERT: A 94 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: A 122 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8548 (tmmt) REVERT: A 204 ASP cc_start: 0.8697 (p0) cc_final: 0.8265 (t0) REVERT: A 546 HIS cc_start: 0.8043 (m90) cc_final: 0.7637 (m90) REVERT: A 551 TYR cc_start: 0.8375 (m-80) cc_final: 0.8091 (m-80) REVERT: A 562 LEU cc_start: 0.8550 (mt) cc_final: 0.8330 (mm) REVERT: A 592 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 718 LEU cc_start: 0.9296 (tm) cc_final: 0.9017 (pp) REVERT: B 41 ASP cc_start: 0.8326 (m-30) cc_final: 0.8043 (m-30) REVERT: B 94 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 122 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8539 (tmmt) REVERT: B 204 ASP cc_start: 0.8694 (p0) cc_final: 0.8253 (t0) REVERT: B 551 TYR cc_start: 0.8393 (m-80) cc_final: 0.8107 (m-80) REVERT: B 562 LEU cc_start: 0.8549 (mt) cc_final: 0.8333 (mm) REVERT: B 576 PHE cc_start: 0.7418 (t80) cc_final: 0.7153 (t80) REVERT: B 584 TYR cc_start: 0.7968 (m-80) cc_final: 0.7573 (m-80) REVERT: B 592 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7881 (tp) REVERT: B 714 PHE cc_start: 0.8402 (t80) cc_final: 0.8148 (t80) REVERT: B 718 LEU cc_start: 0.9351 (tm) cc_final: 0.9059 (pp) outliers start: 23 outliers final: 7 residues processed: 121 average time/residue: 0.7566 time to fit residues: 103.1952 Evaluate side-chains 122 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 592 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 chunk 72 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.140748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.092304 restraints weight = 16089.753| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.99 r_work: 0.3121 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10520 Z= 0.111 Angle : 0.547 8.767 14352 Z= 0.275 Chirality : 0.044 0.221 1714 Planarity : 0.004 0.066 1790 Dihedral : 6.137 47.902 1728 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.09 % Allowed : 19.26 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1288 helix: 1.00 (0.23), residues: 556 sheet: 0.39 (0.28), residues: 290 loop : -1.61 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 317 HIS 0.003 0.001 HIS A 492 PHE 0.012 0.001 PHE A 130 TYR 0.009 0.001 TYR B 584 ARG 0.002 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 12) link_NAG-ASN : angle 1.80814 ( 36) link_BETA1-4 : bond 0.00358 ( 4) link_BETA1-4 : angle 1.18213 ( 12) hydrogen bonds : bond 0.03607 ( 510) hydrogen bonds : angle 4.13812 ( 1476) metal coordination : bond 0.00145 ( 6) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.83912 ( 16) covalent geometry : bond 0.00254 (10490) covalent geometry : angle 0.53872 (14288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.306 Fit side-chains REVERT: A 41 ASP cc_start: 0.8286 (m-30) cc_final: 0.8036 (m-30) REVERT: A 122 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8532 (tmmt) REVERT: A 204 ASP cc_start: 0.8646 (p0) cc_final: 0.8284 (t0) REVERT: A 546 HIS cc_start: 0.8024 (m90) cc_final: 0.7598 (m90) REVERT: A 551 TYR cc_start: 0.8303 (m-80) cc_final: 0.7989 (m-80) REVERT: A 562 LEU cc_start: 0.8523 (mt) cc_final: 0.8291 (mm) REVERT: A 584 TYR cc_start: 0.7938 (m-80) cc_final: 0.7522 (m-80) REVERT: A 592 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7794 (tp) REVERT: A 718 LEU cc_start: 0.9347 (tm) cc_final: 0.9064 (pp) REVERT: B 41 ASP cc_start: 0.8256 (m-30) cc_final: 0.8003 (m-30) REVERT: B 122 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8515 (tmmt) REVERT: B 204 ASP cc_start: 0.8653 (p0) cc_final: 0.8281 (t0) REVERT: B 551 TYR cc_start: 0.8331 (m-80) cc_final: 0.8015 (m-80) REVERT: B 584 TYR cc_start: 0.7939 (m-80) cc_final: 0.7518 (m-80) REVERT: B 718 LEU cc_start: 0.9347 (tm) cc_final: 0.9063 (pp) outliers start: 22 outliers final: 6 residues processed: 127 average time/residue: 0.8165 time to fit residues: 116.9749 Evaluate side-chains 118 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 576 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096104 restraints weight = 16676.117| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.08 r_work: 0.3161 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10520 Z= 0.186 Angle : 0.601 9.140 14352 Z= 0.304 Chirality : 0.045 0.243 1714 Planarity : 0.004 0.068 1790 Dihedral : 6.138 47.285 1728 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.42 % Allowed : 20.30 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1288 helix: 0.96 (0.22), residues: 556 sheet: 0.40 (0.28), residues: 290 loop : -1.61 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.004 0.001 HIS B 492 PHE 0.013 0.001 PHE A 730 TYR 0.016 0.001 TYR B 717 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 1.90575 ( 36) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 1.19340 ( 12) hydrogen bonds : bond 0.04039 ( 510) hydrogen bonds : angle 4.22558 ( 1476) metal coordination : bond 0.00333 ( 6) SS BOND : bond 0.00159 ( 8) SS BOND : angle 0.92438 ( 16) covalent geometry : bond 0.00446 (10490) covalent geometry : angle 0.59292 (14288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8441 (m-30) cc_final: 0.8161 (m-30) REVERT: A 204 ASP cc_start: 0.8740 (p0) cc_final: 0.8474 (t0) REVERT: A 546 HIS cc_start: 0.8099 (m90) cc_final: 0.7712 (m90) REVERT: A 551 TYR cc_start: 0.8510 (m-80) cc_final: 0.8202 (m-80) REVERT: A 562 LEU cc_start: 0.8756 (mt) cc_final: 0.8550 (mm) REVERT: A 584 TYR cc_start: 0.8030 (m-80) cc_final: 0.7673 (m-80) REVERT: A 718 LEU cc_start: 0.9341 (tm) cc_final: 0.9099 (pp) REVERT: A 807 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.6928 (mpp) REVERT: B 41 ASP cc_start: 0.8439 (m-30) cc_final: 0.8166 (m-30) REVERT: B 122 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8539 (tmmt) REVERT: B 204 ASP cc_start: 0.8746 (p0) cc_final: 0.8475 (t0) REVERT: B 551 TYR cc_start: 0.8469 (m-80) cc_final: 0.8137 (m-80) REVERT: B 582 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: B 729 TYR cc_start: 0.8108 (t80) cc_final: 0.7905 (t80) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.8156 time to fit residues: 111.2015 Evaluate side-chains 120 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 709 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 0.0670 chunk 83 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.145604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098175 restraints weight = 16597.243| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.05 r_work: 0.3195 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10520 Z= 0.125 Angle : 0.573 9.100 14352 Z= 0.292 Chirality : 0.044 0.278 1714 Planarity : 0.004 0.064 1790 Dihedral : 5.959 47.538 1728 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.23 % Allowed : 20.78 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1288 helix: 1.06 (0.23), residues: 556 sheet: 0.40 (0.28), residues: 290 loop : -1.53 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 317 HIS 0.003 0.001 HIS B 492 PHE 0.013 0.001 PHE B 730 TYR 0.016 0.001 TYR A 717 ARG 0.002 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 12) link_NAG-ASN : angle 1.76778 ( 36) link_BETA1-4 : bond 0.00330 ( 4) link_BETA1-4 : angle 1.13830 ( 12) hydrogen bonds : bond 0.03769 ( 510) hydrogen bonds : angle 4.16573 ( 1476) metal coordination : bond 0.00139 ( 6) SS BOND : bond 0.00115 ( 8) SS BOND : angle 0.82320 ( 16) covalent geometry : bond 0.00298 (10490) covalent geometry : angle 0.56626 (14288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.103 Fit side-chains REVERT: A 41 ASP cc_start: 0.8364 (m-30) cc_final: 0.8078 (m-30) REVERT: A 122 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8536 (tmmt) REVERT: A 204 ASP cc_start: 0.8694 (p0) cc_final: 0.8449 (t0) REVERT: A 546 HIS cc_start: 0.8070 (m90) cc_final: 0.7660 (m90) REVERT: A 551 TYR cc_start: 0.8474 (m-80) cc_final: 0.8177 (m-80) REVERT: B 41 ASP cc_start: 0.8376 (m-30) cc_final: 0.8102 (m-30) REVERT: B 122 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8527 (tmmt) REVERT: B 204 ASP cc_start: 0.8704 (p0) cc_final: 0.8453 (t0) REVERT: B 551 TYR cc_start: 0.8440 (m-80) cc_final: 0.8152 (m-80) REVERT: B 584 TYR cc_start: 0.8037 (m-80) cc_final: 0.7739 (m-80) REVERT: B 714 PHE cc_start: 0.8351 (t80) cc_final: 0.8132 (t80) REVERT: B 718 LEU cc_start: 0.9262 (tm) cc_final: 0.9013 (pp) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.8352 time to fit residues: 106.2078 Evaluate side-chains 115 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 818 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.145828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098383 restraints weight = 16539.185| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.06 r_work: 0.3192 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10520 Z= 0.135 Angle : 0.588 9.092 14352 Z= 0.296 Chirality : 0.045 0.323 1714 Planarity : 0.004 0.067 1790 Dihedral : 5.901 47.885 1728 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.52 % Allowed : 20.78 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1288 helix: 1.12 (0.23), residues: 556 sheet: 0.43 (0.28), residues: 290 loop : -1.49 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 317 HIS 0.003 0.001 HIS A 492 PHE 0.014 0.001 PHE A 730 TYR 0.012 0.001 TYR A 584 ARG 0.002 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 12) link_NAG-ASN : angle 1.75628 ( 36) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 1.12612 ( 12) hydrogen bonds : bond 0.03807 ( 510) hydrogen bonds : angle 4.16045 ( 1476) metal coordination : bond 0.00175 ( 6) SS BOND : bond 0.00120 ( 8) SS BOND : angle 0.84805 ( 16) covalent geometry : bond 0.00327 (10490) covalent geometry : angle 0.58078 (14288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6618.26 seconds wall clock time: 117 minutes 2.51 seconds (7022.51 seconds total)