Starting phenix.real_space_refine on Wed Sep 17 18:16:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y68_33637/09_2025/7y68_33637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y68_33637/09_2025/7y68_33637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y68_33637/09_2025/7y68_33637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y68_33637/09_2025/7y68_33637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y68_33637/09_2025/7y68_33637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y68_33637/09_2025/7y68_33637.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.57, per 1000 atoms: 0.25 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: 0.74 Conformation dependent library (CDL) restraints added in 400.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.58 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1632 1.30 - 1.43: 2862 1.43 - 1.56: 5902 1.56 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 10490 Sorted by residual: bond pdb=" N ARG A 100 " pdb=" CA ARG A 100 " ideal model delta sigma weight residual 1.455 1.384 0.070 1.25e-02 6.40e+03 3.18e+01 bond pdb=" C ARG B 100 " pdb=" N GLY B 101 " ideal model delta sigma weight residual 1.325 1.265 0.060 1.27e-02 6.20e+03 2.24e+01 bond pdb=" C ARG B 100 " pdb=" O ARG B 100 " ideal model delta sigma weight residual 1.234 1.176 0.057 1.25e-02 6.40e+03 2.10e+01 bond pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 1.524 1.466 0.059 1.31e-02 5.83e+03 2.02e+01 bond pdb=" C ARG A 100 " pdb=" N GLY A 101 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.46e-02 4.69e+03 2.01e+01 ... (remaining 10485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 14081 2.41 - 4.82: 179 4.82 - 7.23: 23 7.23 - 9.64: 4 9.64 - 12.05: 1 Bond angle restraints: 14288 Sorted by residual: angle pdb=" C LEU A 99 " pdb=" N ARG A 100 " pdb=" CA ARG A 100 " ideal model delta sigma weight residual 123.05 111.00 12.05 1.79e+00 3.12e-01 4.53e+01 angle pdb=" N ARG A 100 " pdb=" CA ARG A 100 " pdb=" C ARG A 100 " ideal model delta sigma weight residual 110.14 118.11 -7.97 1.47e+00 4.63e-01 2.94e+01 angle pdb=" C LEU B 99 " pdb=" N ARG B 100 " pdb=" CA ARG B 100 " ideal model delta sigma weight residual 122.74 114.23 8.51 1.82e+00 3.02e-01 2.19e+01 angle pdb=" N ARG B 100 " pdb=" CA ARG B 100 " pdb=" C ARG B 100 " ideal model delta sigma weight residual 110.42 117.50 -7.08 1.55e+00 4.16e-01 2.09e+01 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 117.83 -8.02 2.21e+00 2.05e-01 1.32e+01 ... (remaining 14283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 5760 21.71 - 43.43: 407 43.43 - 65.14: 97 65.14 - 86.86: 38 86.86 - 108.57: 92 Dihedral angle restraints: 6394 sinusoidal: 2570 harmonic: 3824 Sorted by residual: dihedral pdb=" CA PHE A 195 " pdb=" C PHE A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 126.21 53.79 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA PHE B 195 " pdb=" C PHE B 195 " pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta harmonic sigma weight residual 180.00 126.29 53.71 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CB CYS B 197 " pdb=" SG CYS B 197 " pdb=" SG CYS B 256 " pdb=" CB CYS B 256 " ideal model delta sinusoidal sigma weight residual 93.00 162.11 -69.11 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 6391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1686 0.128 - 0.255: 20 0.255 - 0.382: 6 0.382 - 0.510: 1 0.510 - 0.637: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA ARG A 100 " pdb=" N ARG A 100 " pdb=" C ARG A 100 " pdb=" CB ARG A 100 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ARG B 100 " pdb=" N ARG B 100 " pdb=" C ARG B 100 " pdb=" CB ARG B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 27 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1711 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.062 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO B 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 462 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 463 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.030 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1421 2.75 - 3.29: 10036 3.29 - 3.83: 16595 3.83 - 4.36: 20204 4.36 - 4.90: 34093 Nonbonded interactions: 82349 Sorted by model distance: nonbonded pdb=" OD1 ASN A 506 " pdb=" OG SER A 564 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN B 506 " pdb=" OG SER B 564 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A 702 " pdb=" OH TYR A 717 " model vdw 2.220 3.040 nonbonded pdb=" O LEU B 702 " pdb=" OH TYR B 717 " model vdw 2.220 3.040 nonbonded pdb=" NE2 GLN A 472 " pdb=" O VAL A 569 " model vdw 2.227 3.120 ... (remaining 82344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 1.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10520 Z= 0.257 Angle : 0.728 12.054 14352 Z= 0.386 Chirality : 0.052 0.637 1714 Planarity : 0.005 0.093 1790 Dihedral : 22.415 108.571 3894 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.31 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 aren 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 covalent geometry : bond 0.00506 (10490) covalent geometry : angle 0.69983 (14288) SS BOND : bond 0.00126 ( 8) SS BOND : angle 0.91541 ( 16) hydrogen bonds : bond 0.24140 ( 510) hydrogen bonds : angle 8.04533 ( 1476) metal coordination : bond 0.00265 ( 6) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 1.76287 ( 12) link_NAG-ASN : bond 0.00684 ( 12) link_NAG-ASN : angle 3.91198 ( 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 : 0.403 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: 0.4489 time to fit residues: 66.0846 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 : 0.371 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 712 ASN B 476 ASN B 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.136803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089664 restraints weight = 16209.434| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.91 r_work: 0.3050 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10520 Z= 0.189 Angle : 0.744 8.330 14352 Z= 0.361 Chirality : 0.051 0.300 1714 Planarity : 0.005 0.088 1790 Dihedral : 18.089 73.379 1734 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.71 % Allowed : 10.15 % Favored : 88.14 % 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 aren not related in a simple way. whole: -1.42 (0.22), residues: 1288 helix: -0.47 (0.21), residues: 554 sheet: 0.20 (0.30), residues: 278 loop : -2.19 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 114 TYR 0.020 0.002 TYR A 717 PHE 0.023 0.002 PHE A 582 TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00433 (10490) covalent geometry : angle 0.72793 (14288) SS BOND : bond 0.00199 ( 8) SS BOND : angle 0.97887 ( 16) hydrogen bonds : bond 0.05365 ( 510) hydrogen bonds : angle 5.09160 ( 1476) metal coordination : bond 0.00327 ( 6) link_BETA1-4 : bond 0.00139 ( 4) link_BETA1-4 : angle 1.12342 ( 12) link_NAG-ASN : bond 0.00587 ( 12) link_NAG-ASN : angle 3.10171 ( 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 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: 0.8312 (m-30) cc_final: 0.8060 (m-30) REVERT: A 94 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7443 (pp30) REVERT: A 546 HIS cc_start: 0.7970 (m90) cc_final: 0.7636 (m90) REVERT: A 551 TYR cc_start: 0.8132 (m-80) cc_final: 0.7881 (m-80) REVERT: B 41 ASP cc_start: 0.8315 (m-30) cc_final: 0.8060 (m-30) REVERT: B 94 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: B 551 TYR cc_start: 0.8134 (m-80) cc_final: 0.7893 (m-80) REVERT: B 595 TYR cc_start: 0.7758 (t80) cc_final: 0.7138 (t80) outliers start: 18 outliers final: 2 residues processed: 127 average time/residue: 0.3475 time to fit residues: 49.7715 Evaluate side-chains 107 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 476 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.144069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096772 restraints weight = 16598.221| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.95 r_work: 0.3206 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10520 Z= 0.128 Angle : 0.627 9.623 14352 Z= 0.303 Chirality : 0.047 0.303 1714 Planarity : 0.004 0.070 1790 Dihedral : 9.016 59.556 1728 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.99 % Allowed : 12.52 % Favored : 85.48 % 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 aren not related in a simple way. whole: -0.95 (0.23), residues: 1288 helix: 0.08 (0.22), residues: 548 sheet: 0.22 (0.28), residues: 290 loop : -2.04 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 105 TYR 0.009 0.001 TYR A 471 PHE 0.012 0.001 PHE A 576 TRP 0.011 0.001 TRP A 317 HIS 0.003 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00282 (10490) covalent geometry : angle 0.61315 (14288) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.78766 ( 16) hydrogen bonds : bond 0.04349 ( 510) hydrogen bonds : angle 4.47808 ( 1476) metal coordination : bond 0.00182 ( 6) link_BETA1-4 : bond 0.00764 ( 4) link_BETA1-4 : angle 1.35852 ( 12) link_NAG-ASN : bond 0.00665 ( 12) link_NAG-ASN : angle 2.57129 ( 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 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8367 (m-30) cc_final: 0.8085 (m-30) REVERT: A 122 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8667 (tmmt) REVERT: A 204 ASP cc_start: 0.8686 (p0) cc_final: 0.8376 (t0) REVERT: A 546 HIS cc_start: 0.8025 (m90) cc_final: 0.7686 (m90) REVERT: A 551 TYR cc_start: 0.8212 (m-80) cc_final: 0.7970 (m-80) REVERT: A 562 LEU cc_start: 0.8678 (mt) cc_final: 0.8435 (mm) REVERT: A 595 TYR cc_start: 0.7745 (t80) cc_final: 0.7058 (t80) REVERT: B 41 ASP cc_start: 0.8361 (m-30) cc_final: 0.8096 (m-30) REVERT: B 94 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7420 (pp30) REVERT: B 122 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8645 (tmmt) REVERT: B 204 ASP cc_start: 0.8677 (p0) cc_final: 0.8368 (t0) REVERT: B 551 TYR cc_start: 0.8210 (m-80) cc_final: 0.7970 (m-80) REVERT: B 562 LEU cc_start: 0.8688 (mt) cc_final: 0.8427 (mm) REVERT: B 595 TYR cc_start: 0.7801 (t80) cc_final: 0.7049 (t80) outliers start: 21 outliers final: 3 residues processed: 133 average time/residue: 0.3412 time to fit residues: 51.3237 Evaluate side-chains 108 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.0170 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094372 restraints weight = 16698.188| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.94 r_work: 0.3160 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10520 Z= 0.193 Angle : 0.629 9.262 14352 Z= 0.311 Chirality : 0.046 0.282 1714 Planarity : 0.004 0.081 1790 Dihedral : 7.833 56.921 1728 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.37 % Allowed : 14.23 % Favored : 83.40 % 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 aren not related in a simple way. whole: -0.71 (0.23), residues: 1288 helix: 0.33 (0.22), residues: 548 sheet: 0.33 (0.29), residues: 290 loop : -1.99 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 114 TYR 0.014 0.001 TYR A 173 PHE 0.013 0.001 PHE A 730 TRP 0.007 0.001 TRP A 773 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00452 (10490) covalent geometry : angle 0.61474 (14288) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.92627 ( 16) hydrogen bonds : bond 0.04302 ( 510) hydrogen bonds : angle 4.43616 ( 1476) metal coordination : bond 0.00320 ( 6) link_BETA1-4 : bond 0.00335 ( 4) link_BETA1-4 : angle 1.63607 ( 12) link_NAG-ASN : bond 0.00575 ( 12) link_NAG-ASN : angle 2.52360 ( 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 133 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8411 (m-30) cc_final: 0.8168 (m-30) REVERT: A 94 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: A 122 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8670 (tmmt) REVERT: A 546 HIS cc_start: 0.8062 (m90) cc_final: 0.7699 (m90) REVERT: A 551 TYR cc_start: 0.8288 (m-80) cc_final: 0.8041 (m-80) REVERT: A 562 LEU cc_start: 0.8676 (mt) cc_final: 0.8416 (mm) REVERT: A 807 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.6836 (mpp) REVERT: B 41 ASP cc_start: 0.8420 (m-30) cc_final: 0.8176 (m-30) REVERT: B 94 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: B 122 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8676 (tmmt) REVERT: B 551 TYR cc_start: 0.8278 (m-80) cc_final: 0.8026 (m-80) REVERT: B 562 LEU cc_start: 0.8664 (mt) cc_final: 0.8408 (mm) REVERT: B 807 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.6842 (mpp) outliers start: 25 outliers final: 6 residues processed: 123 average time/residue: 0.3637 time to fit residues: 50.1744 Evaluate side-chains 117 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 311 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 689 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 122 LYS Chi-restraints excluded: chain B residue 311 THR 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: 4.9990 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096122 restraints weight = 16667.705| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.02 r_work: 0.3148 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10520 Z= 0.171 Angle : 0.593 8.355 14352 Z= 0.298 Chirality : 0.045 0.265 1714 Planarity : 0.004 0.067 1790 Dihedral : 7.144 51.449 1728 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.23 % Allowed : 15.75 % Favored : 81.02 % 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 aren not related in a simple way. whole: -0.48 (0.23), residues: 1288 helix: 0.56 (0.22), residues: 552 sheet: 0.36 (0.29), residues: 290 loop : -1.87 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 114 TYR 0.012 0.001 TYR B 173 PHE 0.015 0.001 PHE A 576 TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00400 (10490) covalent geometry : angle 0.58071 (14288) SS BOND : bond 0.00145 ( 8) SS BOND : angle 0.90507 ( 16) hydrogen bonds : bond 0.04169 ( 510) hydrogen bonds : angle 4.32125 ( 1476) metal coordination : bond 0.00315 ( 6) link_BETA1-4 : bond 0.00352 ( 4) link_BETA1-4 : angle 1.52078 ( 12) link_NAG-ASN : bond 0.00478 ( 12) link_NAG-ASN : angle 2.29302 ( 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 145 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8446 (m-30) cc_final: 0.8188 (m-30) REVERT: A 94 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: A 122 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8561 (tmmt) REVERT: A 204 ASP cc_start: 0.8736 (p0) cc_final: 0.8422 (t0) REVERT: A 546 HIS cc_start: 0.8079 (m90) cc_final: 0.7708 (m90) REVERT: A 551 TYR cc_start: 0.8454 (m-80) cc_final: 0.8175 (m-80) REVERT: A 562 LEU cc_start: 0.8718 (mt) cc_final: 0.8480 (mm) REVERT: B 41 ASP cc_start: 0.8468 (m-30) cc_final: 0.8208 (m-30) REVERT: B 94 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: B 122 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8571 (tmmt) REVERT: B 204 ASP cc_start: 0.8738 (p0) cc_final: 0.8413 (t0) REVERT: B 551 TYR cc_start: 0.8454 (m-80) cc_final: 0.8169 (m-80) REVERT: B 562 LEU cc_start: 0.8715 (mt) cc_final: 0.8476 (mm) outliers start: 34 outliers final: 8 residues processed: 132 average time/residue: 0.3864 time to fit residues: 57.0888 Evaluate side-chains 120 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 0.0050 chunk 47 optimal weight: 40.0000 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.145724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098024 restraints weight = 16655.899| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.02 r_work: 0.3186 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10520 Z= 0.113 Angle : 0.546 8.426 14352 Z= 0.275 Chirality : 0.044 0.235 1714 Planarity : 0.004 0.071 1790 Dihedral : 6.533 47.743 1728 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.66 % Allowed : 16.79 % Favored : 80.55 % 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 aren not related in a simple way. whole: -0.19 (0.23), residues: 1288 helix: 0.85 (0.22), residues: 556 sheet: 0.38 (0.28), residues: 290 loop : -1.70 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.010 0.001 TYR B 584 PHE 0.012 0.001 PHE A 130 TRP 0.006 0.000 TRP A 317 HIS 0.003 0.000 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00257 (10490) covalent geometry : angle 0.53630 (14288) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.81048 ( 16) hydrogen bonds : bond 0.03708 ( 510) hydrogen bonds : angle 4.16522 ( 1476) metal coordination : bond 0.00129 ( 6) link_BETA1-4 : bond 0.00341 ( 4) link_BETA1-4 : angle 1.38686 ( 12) link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 1.95894 ( 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 142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8391 (m-30) cc_final: 0.8091 (m-30) REVERT: A 94 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: A 122 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8533 (tmmt) REVERT: A 204 ASP cc_start: 0.8637 (p0) cc_final: 0.8385 (t0) REVERT: A 546 HIS cc_start: 0.8067 (m90) cc_final: 0.7703 (m90) REVERT: A 551 TYR cc_start: 0.8406 (m-80) cc_final: 0.8083 (m-80) REVERT: A 562 LEU cc_start: 0.8661 (mt) cc_final: 0.8407 (mm) REVERT: A 807 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7024 (mpp) REVERT: B 41 ASP cc_start: 0.8397 (m-30) cc_final: 0.8096 (m-30) REVERT: B 122 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8538 (tmmt) REVERT: B 204 ASP cc_start: 0.8624 (p0) cc_final: 0.8382 (t0) REVERT: B 551 TYR cc_start: 0.8395 (m-80) cc_final: 0.8088 (m-80) REVERT: B 562 LEU cc_start: 0.8647 (mt) cc_final: 0.8392 (mm) REVERT: B 576 PHE cc_start: 0.7410 (t80) cc_final: 0.7071 (t80) REVERT: B 807 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7039 (mpp) outliers start: 28 outliers final: 7 residues processed: 130 average time/residue: 0.3609 time to fit residues: 52.7965 Evaluate side-chains 121 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.145993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098153 restraints weight = 16653.788| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.12 r_work: 0.3191 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2777 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= 0.124 Angle : 0.555 8.712 14352 Z= 0.280 Chirality : 0.043 0.228 1714 Planarity : 0.004 0.064 1790 Dihedral : 6.260 48.510 1728 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.66 % Allowed : 18.03 % Favored : 79.32 % 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 aren not related in a simple way. whole: -0.04 (0.23), residues: 1288 helix: 0.97 (0.23), residues: 556 sheet: 0.42 (0.28), residues: 290 loop : -1.61 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.011 0.001 TYR B 173 PHE 0.012 0.001 PHE A 130 TRP 0.006 0.001 TRP A 317 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00287 (10490) covalent geometry : angle 0.54587 (14288) SS BOND : bond 0.00115 ( 8) SS BOND : angle 0.81549 ( 16) hydrogen bonds : bond 0.03722 ( 510) hydrogen bonds : angle 4.11813 ( 1476) metal coordination : bond 0.00163 ( 6) link_BETA1-4 : bond 0.00303 ( 4) link_BETA1-4 : angle 1.31010 ( 12) link_NAG-ASN : bond 0.00422 ( 12) link_NAG-ASN : angle 1.85828 ( 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 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8406 (m-30) cc_final: 0.8182 (m-30) REVERT: A 94 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: A 122 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8534 (tmmt) REVERT: A 546 HIS cc_start: 0.8051 (m90) cc_final: 0.7700 (m90) REVERT: A 551 TYR cc_start: 0.8440 (m-80) cc_final: 0.8135 (m-80) REVERT: A 562 LEU cc_start: 0.8699 (mt) cc_final: 0.8490 (mm) REVERT: A 572 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7089 (m-40) REVERT: A 584 TYR cc_start: 0.7922 (m-80) cc_final: 0.7512 (m-80) REVERT: A 718 LEU cc_start: 0.9338 (tm) cc_final: 0.9017 (pp) REVERT: A 729 TYR cc_start: 0.8179 (t80) cc_final: 0.7911 (t80) REVERT: B 41 ASP cc_start: 0.8408 (m-30) cc_final: 0.8184 (m-30) REVERT: B 94 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: B 122 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8539 (tmmt) REVERT: B 204 ASP cc_start: 0.8658 (p0) cc_final: 0.8435 (t0) REVERT: B 551 TYR cc_start: 0.8452 (m-80) cc_final: 0.8142 (m-80) REVERT: B 562 LEU cc_start: 0.8695 (mt) cc_final: 0.8486 (mm) REVERT: B 584 TYR cc_start: 0.7915 (m-80) cc_final: 0.7517 (m-80) REVERT: B 714 PHE cc_start: 0.8358 (t80) cc_final: 0.8122 (t80) REVERT: B 718 LEU cc_start: 0.9339 (tm) cc_final: 0.9030 (pp) outliers start: 28 outliers final: 7 residues processed: 131 average time/residue: 0.3232 time to fit residues: 47.9341 Evaluate side-chains 122 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 689 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 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 689 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: 8.9990 chunk 85 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 121 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.145244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097133 restraints weight = 16523.627| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.10 r_work: 0.3178 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10520 Z= 0.156 Angle : 0.574 8.951 14352 Z= 0.292 Chirality : 0.045 0.245 1714 Planarity : 0.004 0.070 1790 Dihedral : 6.165 48.122 1728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.37 % Allowed : 18.31 % Favored : 79.32 % 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 aren not related in a simple way. whole: 0.02 (0.23), residues: 1288 helix: 0.96 (0.22), residues: 560 sheet: 0.43 (0.28), residues: 290 loop : -1.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.013 0.001 TYR A 173 PHE 0.016 0.001 PHE A 730 TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00372 (10490) covalent geometry : angle 0.56619 (14288) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.82671 ( 16) hydrogen bonds : bond 0.03887 ( 510) hydrogen bonds : angle 4.13119 ( 1476) metal coordination : bond 0.00262 ( 6) link_BETA1-4 : bond 0.00252 ( 4) link_BETA1-4 : angle 1.23259 ( 12) link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 1.83468 ( 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 136 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8375 (m-30) cc_final: 0.8106 (m-30) REVERT: A 94 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: A 122 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8530 (tmmt) REVERT: A 546 HIS cc_start: 0.8041 (m90) cc_final: 0.7676 (m90) REVERT: A 551 TYR cc_start: 0.8456 (m-80) cc_final: 0.8145 (m-80) REVERT: A 562 LEU cc_start: 0.8730 (mt) cc_final: 0.8523 (mm) REVERT: A 572 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7081 (m-40) REVERT: A 575 ASN cc_start: 0.8297 (t0) cc_final: 0.8004 (t160) REVERT: A 718 LEU cc_start: 0.9343 (tm) cc_final: 0.9052 (pp) REVERT: A 729 TYR cc_start: 0.8131 (t80) cc_final: 0.7921 (t80) REVERT: A 807 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6886 (mpp) REVERT: B 41 ASP cc_start: 0.8381 (m-30) cc_final: 0.8171 (m-30) REVERT: B 94 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: B 204 ASP cc_start: 0.8680 (p0) cc_final: 0.8449 (t0) REVERT: B 551 TYR cc_start: 0.8464 (m-80) cc_final: 0.8153 (m-80) REVERT: B 562 LEU cc_start: 0.8749 (mt) cc_final: 0.8547 (mm) REVERT: B 576 PHE cc_start: 0.7511 (t80) cc_final: 0.7122 (t80) REVERT: B 718 LEU cc_start: 0.9335 (tm) cc_final: 0.9033 (pp) REVERT: B 807 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.6862 (mpp) outliers start: 25 outliers final: 9 residues processed: 126 average time/residue: 0.3729 time to fit residues: 52.6904 Evaluate side-chains 123 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 689 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 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 689 MET 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: 6.9990 chunk 50 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.141585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094947 restraints weight = 16309.963| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.89 r_work: 0.3177 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10520 Z= 0.219 Angle : 0.627 9.217 14352 Z= 0.320 Chirality : 0.046 0.249 1714 Planarity : 0.004 0.069 1790 Dihedral : 6.227 46.687 1728 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.09 % Allowed : 19.26 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.24), residues: 1288 helix: 0.92 (0.22), residues: 560 sheet: 0.41 (0.28), residues: 290 loop : -1.55 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.016 0.001 TYR B 173 PHE 0.017 0.002 PHE A 730 TRP 0.006 0.001 TRP A 773 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00526 (10490) covalent geometry : angle 0.61946 (14288) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.93773 ( 16) hydrogen bonds : bond 0.04254 ( 510) hydrogen bonds : angle 4.25625 ( 1476) metal coordination : bond 0.00389 ( 6) link_BETA1-4 : bond 0.00291 ( 4) link_BETA1-4 : angle 1.16909 ( 12) link_NAG-ASN : bond 0.00438 ( 12) link_NAG-ASN : angle 1.93000 ( 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 133 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 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: 0.8389 (m-30) cc_final: 0.8138 (m-30) REVERT: A 94 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 546 HIS cc_start: 0.8073 (m90) cc_final: 0.7696 (m90) REVERT: A 551 TYR cc_start: 0.8440 (m-80) cc_final: 0.8166 (m-80) REVERT: A 562 LEU cc_start: 0.8722 (mt) cc_final: 0.8504 (mm) REVERT: A 575 ASN cc_start: 0.8298 (t0) cc_final: 0.8023 (t160) REVERT: A 714 PHE cc_start: 0.8437 (t80) cc_final: 0.8233 (t80) REVERT: A 718 LEU cc_start: 0.9283 (tm) cc_final: 0.9025 (pp) REVERT: A 807 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.6892 (mpp) REVERT: B 41 ASP cc_start: 0.8396 (m-30) cc_final: 0.8143 (m-30) REVERT: B 204 ASP cc_start: 0.8757 (p0) cc_final: 0.8386 (t0) REVERT: B 551 TYR cc_start: 0.8437 (m-80) cc_final: 0.8160 (m-80) REVERT: B 562 LEU cc_start: 0.8713 (mt) cc_final: 0.8496 (mm) REVERT: B 718 LEU cc_start: 0.9338 (tm) cc_final: 0.9072 (pp) REVERT: B 807 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.6844 (mpp) outliers start: 22 outliers final: 11 residues processed: 120 average time/residue: 0.3887 time to fit residues: 52.3442 Evaluate side-chains 118 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.145935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098502 restraints weight = 16473.747| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.07 r_work: 0.3197 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10520 Z= 0.133 Angle : 0.585 9.075 14352 Z= 0.298 Chirality : 0.045 0.324 1714 Planarity : 0.004 0.065 1790 Dihedral : 5.979 47.101 1728 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % 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 aren not related in a simple way. whole: 0.11 (0.24), residues: 1288 helix: 1.09 (0.23), residues: 556 sheet: 0.41 (0.28), residues: 290 loop : -1.46 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.009 0.001 TYR B 173 PHE 0.016 0.001 PHE A 730 TRP 0.007 0.001 TRP B 317 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00319 (10490) covalent geometry : angle 0.57869 (14288) SS BOND : bond 0.00118 ( 8) SS BOND : angle 0.81550 ( 16) hydrogen bonds : bond 0.03843 ( 510) hydrogen bonds : angle 4.17344 ( 1476) metal coordination : bond 0.00194 ( 6) link_BETA1-4 : bond 0.00314 ( 4) link_BETA1-4 : angle 1.06193 ( 12) link_NAG-ASN : bond 0.00397 ( 12) link_NAG-ASN : angle 1.74573 ( 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 125 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8362 (m-30) cc_final: 0.8102 (m-30) REVERT: A 94 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 122 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8511 (tmmt) REVERT: A 546 HIS cc_start: 0.8060 (m90) cc_final: 0.7669 (m90) REVERT: A 551 TYR cc_start: 0.8443 (m-80) cc_final: 0.8144 (m-80) REVERT: B 41 ASP cc_start: 0.8375 (m-30) cc_final: 0.8102 (m-30) REVERT: B 122 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8519 (tmmt) REVERT: B 204 ASP cc_start: 0.8713 (p0) cc_final: 0.8440 (t0) REVERT: B 551 TYR cc_start: 0.8449 (m-80) cc_final: 0.8157 (m-80) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.3894 time to fit residues: 49.5884 Evaluate side-chains 114 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 818 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.145454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097811 restraints weight = 16658.688| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.08 r_work: 0.3181 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10520 Z= 0.161 Angle : 0.608 9.186 14352 Z= 0.308 Chirality : 0.046 0.261 1714 Planarity : 0.004 0.066 1790 Dihedral : 5.962 47.338 1728 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.42 % Allowed : 20.30 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.24), residues: 1288 helix: 1.08 (0.23), residues: 556 sheet: 0.40 (0.28), residues: 290 loop : -1.44 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.013 0.001 TYR A 584 PHE 0.018 0.001 PHE A 732 TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00388 (10490) covalent geometry : angle 0.60093 (14288) SS BOND : bond 0.00125 ( 8) SS BOND : angle 0.84666 ( 16) hydrogen bonds : bond 0.03919 ( 510) hydrogen bonds : angle 4.17994 ( 1476) metal coordination : bond 0.00270 ( 6) link_BETA1-4 : bond 0.00324 ( 4) link_BETA1-4 : angle 1.06700 ( 12) link_NAG-ASN : bond 0.00390 ( 12) link_NAG-ASN : angle 1.78632 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.73 seconds wall clock time: 55 minutes 1.48 seconds (3301.48 seconds total)