Starting phenix.real_space_refine on Thu Jul 2 21:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_33637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_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_33637/07_2026/7y68_33637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_33637.map" model { file = "/net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_33637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_33637.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_33637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y68_33637/07_2026/7y68_33637.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'PHE:plan': 7, 'TYR:plan': 6, 'GLU:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 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, 'PHE:plan': 7, 'TYR:plan': 6, 'GLU:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 2.45, per 1000 atoms: 0.24 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: 1.18 Conformation dependent library (CDL) restraints added in 387.4 milliseconds 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: 0.35 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: 1.89 Time building geometry restraints manager: 1.52 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 - 17.79: 5468 17.79 - 35.59: 480 35.59 - 53.38: 82 53.38 - 71.17: 20 71.17 - 88.96: 8 Dihedral angle restraints: 6058 sinusoidal: 2234 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 6055 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: 0.03 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: 1.500 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 14.220 88.963 3558 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), 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 ARG 0.007 0.001 ARG B 523 TYR 0.020 0.002 TYR A 729 PHE 0.013 0.002 PHE A 764 TRP 0.011 0.001 TRP B 634 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.26 (10490) covalent geometry : angle 0.69983 / 0.38 (14288) SS BOND : bond 0.00126 / 0.09 ( 8) SS BOND : angle 0.91541 / 0.63 ( 16) hydrogen bonds : bond 0.24140 / 16.44 ( 510) hydrogen bonds : angle 8.04533 / 5.48 ( 1476) metal coordination : bond 0.00265 / 0.18 ( 6) link_BETA1-4 : bond 0.00405 / 0.27 ( 4) link_BETA1-4 : angle 1.76287 / 1.42 ( 12) link_NAG-ASN : bond 0.00684 / 0.48 ( 12) link_NAG-ASN : angle 3.91198 / 2.95 ( 36) *********************** 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 : 0.404 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: 0.4295 time to fit residues: 63.5452 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 : 0.408 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3887 r_free = 0.3887 target = 0.136867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089893 restraints weight = 16233.786| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.92 r_work: 0.3047 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1393 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= 0.187 Angle : 0.670 8.485 14352 Z= 0.344 Chirality : 0.048 0.297 1714 Planarity : 0.005 0.088 1790 Dihedral : 5.956 49.755 1398 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.71 % Allowed : 9.87 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.22), residues: 1288 helix: -0.58 (0.21), residues: 548 sheet: 0.21 (0.30), residues: 278 loop : -2.18 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 114 TYR 0.020 0.001 TYR A 717 PHE 0.020 0.002 PHE A 582 TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10490) covalent geometry : angle 0.64973 / 0.34 (14288) SS BOND : bond 0.00197 / 0.13 ( 8) SS BOND : angle 0.97944 / 0.61 ( 16) hydrogen bonds : bond 0.05702 / 3.80 ( 510) hydrogen bonds : angle 5.17060 / 3.49 ( 1476) metal coordination : bond 0.00306 / 0.21 ( 6) link_BETA1-4 : bond 0.00180 / 0.12 ( 4) link_BETA1-4 : angle 0.98581 / 0.79 ( 12) link_NAG-ASN : bond 0.00620 / 0.43 ( 12) link_NAG-ASN : angle 3.27638 / 2.51 ( 36) *********************** 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 127 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8328 (m-30) cc_final: 0.8065 (m-30) REVERT: A 94 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: A 546 HIS cc_start: 0.7964 (m90) cc_final: 0.7607 (m90) REVERT: A 551 TYR cc_start: 0.8129 (m-80) cc_final: 0.7889 (m-80) REVERT: A 595 TYR cc_start: 0.7762 (t80) cc_final: 0.7136 (t80) REVERT: B 41 ASP cc_start: 0.8330 (m-30) cc_final: 0.8089 (m-30) REVERT: B 94 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7505 (pp30) REVERT: B 551 TYR cc_start: 0.8133 (m-80) cc_final: 0.7895 (m-80) REVERT: B 595 TYR cc_start: 0.7777 (t80) cc_final: 0.7143 (t80) outliers start: 18 outliers final: 2 residues processed: 119 average time/residue: 0.3817 time to fit residues: 50.7842 Evaluate side-chains 103 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 94 GLN 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 107 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3922 r_free = 0.3922 target = 0.138648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.091856 restraints weight = 16185.552| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.88 r_work: 0.3109 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1745 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= 0.189 Angle : 0.612 9.546 14352 Z= 0.314 Chirality : 0.047 0.295 1714 Planarity : 0.005 0.079 1790 Dihedral : 5.536 47.137 1392 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.71 % Allowed : 12.62 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.23), residues: 1288 helix: -0.09 (0.22), residues: 548 sheet: 0.14 (0.29), residues: 290 loop : -2.17 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 114 TYR 0.013 0.002 TYR A 173 PHE 0.013 0.001 PHE B 730 TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10490) covalent geometry : angle 0.59530 / 0.31 (14288) SS BOND : bond 0.00165 / 0.11 ( 8) SS BOND : angle 0.95436 / 0.58 ( 16) hydrogen bonds : bond 0.04900 / 3.29 ( 510) hydrogen bonds : angle 4.71163 / 3.18 ( 1476) metal coordination : bond 0.00360 / 0.25 ( 6) link_BETA1-4 : bond 0.00261 / 0.18 ( 4) link_BETA1-4 : angle 1.09342 / 0.90 ( 12) link_NAG-ASN : bond 0.00543 / 0.37 ( 12) link_NAG-ASN : angle 2.83592 / 2.18 ( 36) *********************** 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 135 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8439 (m-30) cc_final: 0.8217 (m-30) REVERT: A 94 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7316 (pp30) REVERT: A 122 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8709 (tmmm) REVERT: A 153 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7523 (p0) REVERT: A 546 HIS cc_start: 0.8049 (m90) cc_final: 0.7689 (m90) REVERT: A 551 TYR cc_start: 0.8158 (m-80) cc_final: 0.7896 (m-80) REVERT: A 583 MET cc_start: 0.8877 (mtm) cc_final: 0.8673 (mtm) REVERT: B 41 ASP cc_start: 0.8440 (m-30) cc_final: 0.8167 (m-30) REVERT: B 94 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7374 (pp30) REVERT: B 153 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 551 TYR cc_start: 0.8155 (m-80) cc_final: 0.7893 (m-80) outliers start: 18 outliers final: 2 residues processed: 130 average time/residue: 0.3408 time to fit residues: 50.1021 Evaluate side-chains 113 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 153 ASP Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 153 ASP 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 62 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 572 ASN B 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.137617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090346 restraints weight = 16176.591| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.85 r_work: 0.3062 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10520 Z= 0.236 Angle : 0.633 9.979 14352 Z= 0.323 Chirality : 0.048 0.311 1714 Planarity : 0.005 0.082 1790 Dihedral : 5.482 46.718 1392 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.56 % Allowed : 14.90 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1288 helix: 0.20 (0.22), residues: 550 sheet: 0.20 (0.29), residues: 290 loop : -2.15 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 114 TYR 0.015 0.002 TYR B 173 PHE 0.014 0.002 PHE A 730 TRP 0.009 0.001 TRP B 773 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (10490) covalent geometry : angle 0.61804 / 0.32 (14288) SS BOND : bond 0.00203 / 0.13 ( 8) SS BOND : angle 1.11939 / 0.72 ( 16) hydrogen bonds : bond 0.04742 / 3.19 ( 510) hydrogen bonds : angle 4.61589 / 3.12 ( 1476) metal coordination : bond 0.00452 / 0.32 ( 6) link_BETA1-4 : bond 0.00241 / 0.16 ( 4) link_BETA1-4 : angle 1.21595 / 1.00 ( 12) link_NAG-ASN : bond 0.00523 / 0.34 ( 12) link_NAG-ASN : angle 2.70706 / 2.07 ( 36) *********************** 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 134 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8471 (m-30) cc_final: 0.8223 (m-30) REVERT: A 94 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: A 122 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8707 (tmmm) REVERT: A 153 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7481 (p0) REVERT: A 546 HIS cc_start: 0.8098 (m90) cc_final: 0.7714 (m90) REVERT: A 551 TYR cc_start: 0.8281 (m-80) cc_final: 0.8000 (m-80) REVERT: A 595 TYR cc_start: 0.7773 (t80) cc_final: 0.7085 (t80) REVERT: A 807 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.6771 (mpp) REVERT: B 41 ASP cc_start: 0.8481 (m-30) cc_final: 0.8237 (m-30) REVERT: B 94 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: B 153 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7489 (p0) REVERT: B 551 TYR cc_start: 0.8276 (m-80) cc_final: 0.7984 (m-80) REVERT: B 595 TYR cc_start: 0.7777 (t80) cc_final: 0.7078 (t80) REVERT: B 807 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.6843 (mpp) outliers start: 27 outliers final: 8 residues processed: 124 average time/residue: 0.3987 time to fit residues: 55.1234 Evaluate side-chains 114 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 153 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 195 PHE 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 94 GLN 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 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 96 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.091649 restraints weight = 16087.615| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.86 r_work: 0.3085 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10520 Z= 0.163 Angle : 0.582 9.997 14352 Z= 0.296 Chirality : 0.046 0.284 1714 Planarity : 0.004 0.071 1790 Dihedral : 5.258 44.476 1392 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.56 % Allowed : 15.65 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1288 helix: 0.37 (0.22), residues: 552 sheet: 0.23 (0.29), residues: 290 loop : -2.04 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 523 TYR 0.011 0.001 TYR A 173 PHE 0.013 0.001 PHE A 730 TRP 0.007 0.001 TRP A 317 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (10490) covalent geometry : angle 0.56881 / 0.29 (14288) SS BOND : bond 0.00117 / 0.08 ( 8) SS BOND : angle 0.91399 / 0.55 ( 16) hydrogen bonds : bond 0.04245 / 2.86 ( 510) hydrogen bonds : angle 4.42070 / 2.99 ( 1476) metal coordination : bond 0.00279 / 0.19 ( 6) link_BETA1-4 : bond 0.00319 / 0.19 ( 4) link_BETA1-4 : angle 1.03311 / 0.83 ( 12) link_NAG-ASN : bond 0.00480 / 0.33 ( 12) link_NAG-ASN : angle 2.42227 / 1.87 ( 36) *********************** 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 140 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8371 (m-30) cc_final: 0.8131 (m-30) REVERT: A 153 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7492 (p0) REVERT: A 546 HIS cc_start: 0.8071 (m90) cc_final: 0.7688 (m90) REVERT: A 551 TYR cc_start: 0.8335 (m-80) cc_final: 0.8038 (m-80) REVERT: A 562 LEU cc_start: 0.8538 (mt) cc_final: 0.8269 (mm) REVERT: A 583 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8585 (mmm) REVERT: A 592 LEU cc_start: 0.8213 (mm) cc_final: 0.7803 (tp) REVERT: A 807 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.6682 (mpp) REVERT: B 41 ASP cc_start: 0.8381 (m-30) cc_final: 0.8145 (m-30) REVERT: B 94 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: B 153 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 551 TYR cc_start: 0.8328 (m-80) cc_final: 0.8027 (m-80) REVERT: B 562 LEU cc_start: 0.8549 (mt) cc_final: 0.8294 (mm) REVERT: B 592 LEU cc_start: 0.8243 (mm) cc_final: 0.7759 (tp) REVERT: B 807 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.6835 (mpp) outliers start: 27 outliers final: 7 residues processed: 126 average time/residue: 0.3319 time to fit residues: 47.0701 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 : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 MET 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 121 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.139461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.092345 restraints weight = 16208.489| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.87 r_work: 0.3098 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10520 Z= 0.144 Angle : 0.569 10.174 14352 Z= 0.288 Chirality : 0.045 0.263 1714 Planarity : 0.004 0.074 1790 Dihedral : 5.069 42.892 1392 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.18 % Allowed : 17.74 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1288 helix: 0.71 (0.22), residues: 556 sheet: 0.32 (0.29), residues: 290 loop : -1.81 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.011 0.001 TYR A 173 PHE 0.013 0.001 PHE A 730 TRP 0.008 0.001 TRP B 317 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10490) covalent geometry : angle 0.55737 / 0.29 (14288) SS BOND : bond 0.00116 / 0.08 ( 8) SS BOND : angle 0.86611 / 0.52 ( 16) hydrogen bonds : bond 0.04019 / 2.72 ( 510) hydrogen bonds : angle 4.28822 / 2.90 ( 1476) metal coordination : bond 0.00230 / 0.16 ( 6) link_BETA1-4 : bond 0.00304 / 0.20 ( 4) link_BETA1-4 : angle 1.03648 / 0.83 ( 12) link_NAG-ASN : bond 0.00467 / 0.33 ( 12) link_NAG-ASN : angle 2.24170 / 1.74 ( 36) *********************** 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 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8362 (m-30) cc_final: 0.8099 (m-30) REVERT: A 94 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: A 153 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7502 (p0) REVERT: A 204 ASP cc_start: 0.8673 (p0) cc_final: 0.8241 (t0) REVERT: A 546 HIS cc_start: 0.8037 (m90) cc_final: 0.7649 (m90) REVERT: A 551 TYR cc_start: 0.8327 (m-80) cc_final: 0.8034 (m-80) REVERT: A 562 LEU cc_start: 0.8556 (mt) cc_final: 0.8313 (mm) REVERT: A 592 LEU cc_start: 0.8216 (mm) cc_final: 0.7707 (tp) REVERT: B 41 ASP cc_start: 0.8375 (m-30) cc_final: 0.8119 (m-30) REVERT: B 94 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: B 153 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 204 ASP cc_start: 0.8682 (p0) cc_final: 0.8243 (t0) REVERT: B 551 TYR cc_start: 0.8323 (m-80) cc_final: 0.8035 (m-80) REVERT: B 562 LEU cc_start: 0.8536 (mt) cc_final: 0.8302 (mm) REVERT: B 592 LEU cc_start: 0.8244 (mm) cc_final: 0.7718 (tp) REVERT: B 807 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.6898 (mpp) outliers start: 23 outliers final: 4 residues processed: 130 average time/residue: 0.3145 time to fit residues: 46.4148 Evaluate side-chains 122 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 153 ASP 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 153 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 0.0060 chunk 5 optimal weight: 0.0980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3928 r_free = 0.3928 target = 0.139785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.092420 restraints weight = 16121.327| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.90 r_work: 0.3097 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10520 Z= 0.113 Angle : 0.543 9.299 14352 Z= 0.275 Chirality : 0.044 0.243 1714 Planarity : 0.004 0.064 1790 Dihedral : 4.836 39.661 1392 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.52 % Allowed : 19.26 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.23), residues: 1288 helix: 0.91 (0.22), residues: 556 sheet: 0.37 (0.28), residues: 290 loop : -1.71 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 321 TYR 0.010 0.001 TYR B 584 PHE 0.012 0.001 PHE A 130 TRP 0.009 0.001 TRP B 317 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10490) covalent geometry : angle 0.53277 / 0.27 (14288) SS BOND : bond 0.00116 / 0.08 ( 8) SS BOND : angle 0.80482 / 0.48 ( 16) hydrogen bonds : bond 0.03650 / 2.46 ( 510) hydrogen bonds : angle 4.18356 / 2.82 ( 1476) metal coordination : bond 0.00140 / 0.10 ( 6) link_BETA1-4 : bond 0.00299 / 0.21 ( 4) link_BETA1-4 : angle 0.93400 / 0.71 ( 12) link_NAG-ASN : bond 0.00424 / 0.30 ( 12) link_NAG-ASN : angle 2.05367 / 1.62 ( 36) *********************** 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 131 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8302 (m-30) cc_final: 0.8017 (m-30) REVERT: A 204 ASP cc_start: 0.8626 (p0) cc_final: 0.8251 (t0) REVERT: A 546 HIS cc_start: 0.8011 (m90) cc_final: 0.7607 (m90) REVERT: A 551 TYR cc_start: 0.8317 (m-80) cc_final: 0.7989 (m-80) REVERT: A 562 LEU cc_start: 0.8503 (mt) cc_final: 0.8287 (mm) REVERT: A 584 TYR cc_start: 0.7881 (m-80) cc_final: 0.7462 (m-80) REVERT: A 714 PHE cc_start: 0.8487 (t80) cc_final: 0.8218 (t80) REVERT: A 718 LEU cc_start: 0.9326 (tm) cc_final: 0.9019 (pp) REVERT: B 41 ASP cc_start: 0.8302 (m-30) cc_final: 0.8019 (m-30) REVERT: B 204 ASP cc_start: 0.8633 (p0) cc_final: 0.8257 (t0) REVERT: B 551 TYR cc_start: 0.8320 (m-80) cc_final: 0.7988 (m-80) REVERT: B 562 LEU cc_start: 0.8511 (mt) cc_final: 0.8305 (mm) REVERT: B 584 TYR cc_start: 0.7889 (m-80) cc_final: 0.7533 (m-80) REVERT: B 718 LEU cc_start: 0.9332 (tm) cc_final: 0.9036 (pp) REVERT: B 807 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.6846 (mpp) outliers start: 16 outliers final: 5 residues processed: 124 average time/residue: 0.3181 time to fit residues: 44.7025 Evaluate side-chains 120 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3879 r_free = 0.3879 target = 0.136413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087734 restraints weight = 16241.913| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.97 r_work: 0.3028 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10520 Z= 0.228 Angle : 0.626 9.201 14352 Z= 0.316 Chirality : 0.047 0.269 1714 Planarity : 0.004 0.076 1790 Dihedral : 5.066 40.230 1392 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.61 % Allowed : 19.92 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1288 helix: 0.89 (0.22), residues: 556 sheet: 0.36 (0.29), residues: 290 loop : -1.70 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.017 0.002 TYR A 173 PHE 0.015 0.002 PHE A 730 TRP 0.007 0.001 TRP A 320 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (10490) covalent geometry : angle 0.61593 / 0.31 (14288) SS BOND : bond 0.00201 / 0.13 ( 8) SS BOND : angle 1.01043 / 0.60 ( 16) hydrogen bonds : bond 0.04171 / 2.83 ( 510) hydrogen bonds : angle 4.28996 / 2.90 ( 1476) metal coordination : bond 0.00425 / 0.30 ( 6) link_BETA1-4 : bond 0.00168 / 0.12 ( 4) link_BETA1-4 : angle 1.27078 / 1.03 ( 12) link_NAG-ASN : bond 0.00467 / 0.30 ( 12) link_NAG-ASN : angle 2.19473 / 1.72 ( 36) *********************** 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 129 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8296 (m-30) cc_final: 0.8005 (m-30) REVERT: A 204 ASP cc_start: 0.8682 (p0) cc_final: 0.8209 (t0) REVERT: A 546 HIS cc_start: 0.8065 (m90) cc_final: 0.7627 (m90) REVERT: A 551 TYR cc_start: 0.8297 (m-80) cc_final: 0.8010 (m-80) REVERT: A 562 LEU cc_start: 0.8494 (mt) cc_final: 0.8241 (mm) REVERT: A 807 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.6695 (mpp) REVERT: B 41 ASP cc_start: 0.8328 (m-30) cc_final: 0.8081 (m-30) REVERT: B 94 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: B 204 ASP cc_start: 0.8682 (p0) cc_final: 0.8204 (t0) REVERT: B 551 TYR cc_start: 0.8302 (m-80) cc_final: 0.8009 (m-80) REVERT: B 562 LEU cc_start: 0.8487 (mt) cc_final: 0.8238 (mm) REVERT: B 807 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.6804 (mpp) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 0.2777 time to fit residues: 38.9946 Evaluate side-chains 118 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3881 r_free = 0.3881 target = 0.136410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088757 restraints weight = 16075.880| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.89 r_work: 0.3037 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10520 Z= 0.183 Angle : 0.605 9.077 14352 Z= 0.306 Chirality : 0.046 0.267 1714 Planarity : 0.004 0.065 1790 Dihedral : 5.049 39.543 1392 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.33 % Allowed : 20.30 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1288 helix: 0.88 (0.22), residues: 560 sheet: 0.30 (0.28), residues: 290 loop : -1.65 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 66 TYR 0.014 0.001 TYR A 173 PHE 0.014 0.001 PHE A 730 TRP 0.008 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (10490) covalent geometry : angle 0.59496 / 0.30 (14288) SS BOND : bond 0.00161 / 0.10 ( 8) SS BOND : angle 0.94000 / 0.55 ( 16) hydrogen bonds : bond 0.04050 / 2.75 ( 510) hydrogen bonds : angle 4.31265 / 2.90 ( 1476) metal coordination : bond 0.00338 / 0.24 ( 6) link_BETA1-4 : bond 0.00274 / 0.18 ( 4) link_BETA1-4 : angle 1.12469 / 0.90 ( 12) link_NAG-ASN : bond 0.00443 / 0.30 ( 12) link_NAG-ASN : angle 2.13989 / 1.67 ( 36) *********************** 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 121 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8301 (m-30) cc_final: 0.8034 (m-30) REVERT: A 204 ASP cc_start: 0.8706 (p0) cc_final: 0.8178 (t0) REVERT: A 320 TRP cc_start: 0.7095 (t60) cc_final: 0.6688 (m-10) REVERT: A 546 HIS cc_start: 0.8065 (m90) cc_final: 0.7663 (m90) REVERT: A 551 TYR cc_start: 0.8319 (m-80) cc_final: 0.8042 (m-80) REVERT: A 562 LEU cc_start: 0.8498 (mt) cc_final: 0.8278 (mm) REVERT: A 576 PHE cc_start: 0.7503 (t80) cc_final: 0.7274 (t80) REVERT: A 714 PHE cc_start: 0.8453 (t80) cc_final: 0.8249 (t80) REVERT: A 718 LEU cc_start: 0.9257 (tm) cc_final: 0.8972 (pp) REVERT: A 807 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.6574 (mpp) REVERT: B 41 ASP cc_start: 0.8318 (m-30) cc_final: 0.8049 (m-30) REVERT: B 551 TYR cc_start: 0.8318 (m-80) cc_final: 0.8018 (m-80) REVERT: B 562 LEU cc_start: 0.8505 (mt) cc_final: 0.8284 (mm) REVERT: B 576 PHE cc_start: 0.7436 (t80) cc_final: 0.7235 (t80) REVERT: B 718 LEU cc_start: 0.9304 (tm) cc_final: 0.9039 (pp) REVERT: B 807 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.6763 (mpp) outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 0.2910 time to fit residues: 38.2857 Evaluate side-chains 116 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 572 ASN 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 167 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090797 restraints weight = 16098.600| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.96 r_work: 0.3072 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10520 Z= 0.122 Angle : 0.571 9.061 14352 Z= 0.288 Chirality : 0.044 0.235 1714 Planarity : 0.004 0.068 1790 Dihedral : 4.792 37.295 1392 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.04 % Allowed : 20.59 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1288 helix: 1.02 (0.23), residues: 554 sheet: 0.34 (0.28), residues: 290 loop : -1.54 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.009 0.001 TYR A 173 PHE 0.012 0.001 PHE B 130 TRP 0.007 0.001 TRP A 317 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (10490) covalent geometry : angle 0.56208 / 0.29 (14288) SS BOND : bond 0.00115 / 0.08 ( 8) SS BOND : angle 0.85965 / 0.50 ( 16) hydrogen bonds : bond 0.03641 / 2.46 ( 510) hydrogen bonds : angle 4.18173 / 2.81 ( 1476) metal coordination : bond 0.00178 / 0.12 ( 6) link_BETA1-4 : bond 0.00413 / 0.26 ( 4) link_BETA1-4 : angle 0.91317 / 0.70 ( 12) link_NAG-ASN : bond 0.00435 / 0.31 ( 12) link_NAG-ASN : angle 1.95301 / 1.52 ( 36) ********************** 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 126 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8241 (m-30) cc_final: 0.7959 (m-30) REVERT: A 204 ASP cc_start: 0.8604 (p0) cc_final: 0.8221 (t0) REVERT: A 546 HIS cc_start: 0.8047 (m90) cc_final: 0.7621 (m90) REVERT: A 551 TYR cc_start: 0.8276 (m-80) cc_final: 0.7980 (m-80) REVERT: A 562 LEU cc_start: 0.8491 (mt) cc_final: 0.8288 (mm) REVERT: A 576 PHE cc_start: 0.7372 (t80) cc_final: 0.7073 (t80) REVERT: A 595 TYR cc_start: 0.7663 (t80) cc_final: 0.6962 (t80) REVERT: A 718 LEU cc_start: 0.9321 (tm) cc_final: 0.9013 (pp) REVERT: B 41 ASP cc_start: 0.8249 (m-30) cc_final: 0.7968 (m-30) REVERT: B 204 ASP cc_start: 0.8627 (p0) cc_final: 0.8229 (t0) REVERT: B 551 TYR cc_start: 0.8275 (m-80) cc_final: 0.7977 (m-80) REVERT: B 572 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.6988 (m-40) REVERT: B 576 PHE cc_start: 0.7310 (t80) cc_final: 0.7039 (t80) REVERT: B 595 TYR cc_start: 0.7669 (t80) cc_final: 0.6974 (t80) REVERT: B 718 LEU cc_start: 0.9302 (tm) cc_final: 0.9019 (pp) REVERT: B 807 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6700 (mpp) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.3028 time to fit residues: 42.8356 Evaluate side-chains 120 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 572 ASN 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 572 ASN Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 807 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 71 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3900 r_free = 0.3900 target = 0.137976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089453 restraints weight = 16268.716| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.97 r_work: 0.3054 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10520 Z= 0.168 Angle : 0.599 9.245 14352 Z= 0.302 Chirality : 0.046 0.243 1714 Planarity : 0.004 0.067 1790 Dihedral : 4.840 37.196 1392 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.04 % Allowed : 21.35 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1288 helix: 1.00 (0.23), residues: 554 sheet: 0.37 (0.28), residues: 290 loop : -1.46 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.014 0.001 TYR A 173 PHE 0.013 0.001 PHE A 730 TRP 0.005 0.001 TRP A 317 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (10490) covalent geometry : angle 0.59016 / 0.30 (14288) SS BOND : bond 0.00167 / 0.11 ( 8) SS BOND : angle 0.89952 / 0.53 ( 16) hydrogen bonds : bond 0.03818 / 2.58 ( 510) hydrogen bonds : angle 4.18413 / 2.81 ( 1476) metal coordination : bond 0.00286 / 0.20 ( 6) link_BETA1-4 : bond 0.00389 / 0.24 ( 4) link_BETA1-4 : angle 1.09244 / 0.89 ( 12) link_NAG-ASN : bond 0.00415 / 0.28 ( 12) link_NAG-ASN : angle 2.01009 / 1.57 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2803.22 seconds wall clock time: 48 minutes 43.78 seconds (2923.78 seconds total)