Starting phenix.real_space_refine on Thu Jul 2 19:46:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y63_33632/07_2026/7y63_33632.map" } resolution = 3.16 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= 0.001 sd= 0.061 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 66 5.16 5 C 6430 2.51 5 N 1604 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9924 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4863 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'TYR:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4863 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'TYR:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.02, per 1000 atoms: 0.20 Number of scatterers: 9924 At special positions: 0 Unit cell: (108.692, 80.1467, 133.944, 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 66 16.00 O 1822 8.00 N 1604 7.00 C 6430 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=2.04 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=2.04 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 B 902 " - " ASN B 27 " " NAG B 903 " - " ASN B 141 " " NAG B 904 " - " ASN B 123 " " 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: 0.76 Conformation dependent library (CDL) restraints added in 248.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 568 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 568 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 45.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.538A pdb=" N VAL A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 479 removed outlier: 3.579A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix removed outlier: 3.916A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.617A pdb=" N LEU A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'A' and resid 506 through 533 removed outlier: 3.972A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.538A pdb=" N MET A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 4.578A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 626 Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.851A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.966A pdb=" N LEU A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.906A pdb=" N LEU A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.556A pdb=" N CYS A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 755 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 763 " --> pdb=" O TRP A 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 818 removed outlier: 3.918A pdb=" N SER A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 813 " --> pdb=" O GLY A 809 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.538A pdb=" N VAL B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 479 removed outlier: 3.580A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.917A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.617A pdb=" N LEU B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 505' Processing helix chain 'B' and resid 506 through 533 removed outlier: 3.972A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 529 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 531 " --> pdb=" O HIS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 549 through 561 removed outlier: 3.539A pdb=" N MET B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 4.578A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 626 Processing helix chain 'B' and resid 630 through 652 removed outlier: 3.850A pdb=" N THR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.966A pdb=" N LEU B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 693 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.907A pdb=" N LEU B 728 " --> pdb=" O CYS B 724 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 736 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 769 removed outlier: 3.555A pdb=" N CYS B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 763 " --> pdb=" O TRP B 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 794 through 818 removed outlier: 3.918A pdb=" N SER B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 813 " --> pdb=" O GLY B 809 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.849A pdb=" N ASP A 41 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.910A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.602A pdb=" N PHE A 164 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 285 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.473A pdb=" N CYS A 197 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 43 removed outlier: 3.849A pdb=" N ASP B 41 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 115 Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.910A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.601A pdb=" N PHE B 164 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 285 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.472A pdb=" N CYS B 197 " --> pdb=" O LYS B 250 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1386 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: 1.55 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3094 1.34 - 1.46: 2472 1.46 - 1.58: 4476 1.58 - 1.70: 0 1.70 - 1.83: 98 Bond restraints: 10140 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CA ARG B 85 " pdb=" CB ARG B 85 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.39e-02 5.18e+03 3.91e+00 bond pdb=" CA ARG A 85 " pdb=" CB ARG A 85 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.39e-02 5.18e+03 3.91e+00 bond pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.80e-02 3.09e+03 2.60e+00 ... (remaining 10135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13203 1.53 - 3.06: 487 3.06 - 4.60: 77 4.60 - 6.13: 15 6.13 - 7.66: 6 Bond angle restraints: 13788 Sorted by residual: angle pdb=" C ALA A 715 " pdb=" CA ALA A 715 " pdb=" CB ALA A 715 " ideal model delta sigma weight residual 110.88 116.78 -5.90 1.57e+00 4.06e-01 1.41e+01 angle pdb=" N PHE A 195 " pdb=" CA PHE A 195 " pdb=" C PHE A 195 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N PHE B 195 " pdb=" CA PHE B 195 " pdb=" C PHE B 195 " ideal model delta sigma weight residual 109.81 117.46 -7.65 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N SER A 716 " pdb=" CA SER A 716 " pdb=" C SER A 716 " ideal model delta sigma weight residual 111.75 115.84 -4.09 1.28e+00 6.10e-01 1.02e+01 angle pdb=" C ALA B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta sigma weight residual 121.80 114.40 7.40 2.44e+00 1.68e-01 9.19e+00 ... (remaining 13783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5278 17.57 - 35.15: 456 35.15 - 52.72: 102 52.72 - 70.30: 14 70.30 - 87.87: 16 Dihedral angle restraints: 5866 sinusoidal: 2232 harmonic: 3634 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 180.00 127.86 52.14 0 5.00e+00 4.00e-02 1.09e+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 180.00 127.89 52.11 0 5.00e+00 4.00e-02 1.09e+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 93.00 172.68 -79.68 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 5863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1574 0.104 - 0.207: 61 0.207 - 0.311: 5 0.311 - 0.415: 2 0.415 - 0.519: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1641 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 195 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO A 196 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 195 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO B 196 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 78 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 79 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.036 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1457 2.75 - 3.29: 9676 3.29 - 3.83: 15673 3.83 - 4.36: 19202 4.36 - 4.90: 32813 Nonbonded interactions: 78821 Sorted by model distance: nonbonded pdb=" NH2 ARG A 59 " pdb=" O LYS A 122 " model vdw 2.214 3.120 nonbonded pdb=" NH2 ARG B 59 " pdb=" O LYS B 122 " model vdw 2.214 3.120 nonbonded pdb=" O THR A 224 " pdb=" NH1 ARG A 781 " model vdw 2.221 3.120 nonbonded pdb=" O THR B 224 " pdb=" NH1 ARG B 781 " model vdw 2.221 3.120 nonbonded pdb=" CD2 LEU A 81 " pdb=" CG2 VAL B 90 " model vdw 2.228 3.880 ... (remaining 78816 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.530 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.006 0.083 10168 Z= 0.249 Angle : 0.739 9.947 13846 Z= 0.391 Chirality : 0.053 0.519 1644 Planarity : 0.005 0.098 1718 Dihedral : 14.637 87.870 3490 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1218 helix: -1.22 (0.23), residues: 468 sheet: -1.13 (0.30), residues: 296 loop : -1.79 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.018 0.002 TYR A 173 PHE 0.016 0.002 PHE A 576 TRP 0.008 0.001 TRP B 700 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (10140) covalent geometry : angle 0.70238 / 0.38 (13788) SS BOND : bond 0.00295 / 0.19 ( 8) SS BOND : angle 1.50042 / 0.94 ( 16) hydrogen bonds : bond 0.26634 / 17.80 ( 478) hydrogen bonds : angle 9.30574 / 6.40 ( 1386) metal coordination : bond 0.00190 / 0.12 ( 6) link_BETA1-4 : bond 0.00878 / 0.54 ( 4) link_BETA1-4 : angle 2.29671 / 1.39 ( 12) link_NAG-ASN : bond 0.00798 / 0.49 ( 10) link_NAG-ASN : angle 4.72251 / 3.03 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.226 Fit side-chains REVERT: A 694 MET cc_start: 0.5732 (mpp) cc_final: 0.5361 (mpp) REVERT: A 728 LEU cc_start: 0.9087 (mt) cc_final: 0.8840 (mt) REVERT: A 749 LEU cc_start: 0.8529 (tp) cc_final: 0.8255 (pp) REVERT: B 694 MET cc_start: 0.5776 (mpp) cc_final: 0.5413 (mpp) REVERT: B 728 LEU cc_start: 0.9073 (mt) cc_final: 0.8828 (mt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0776 time to fit residues: 17.3601 Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 ASN A 774 GLN B 699 ASN B 774 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.159789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105655 restraints weight = 13694.682| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.78 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10168 Z= 0.212 Angle : 0.725 11.753 13846 Z= 0.365 Chirality : 0.048 0.292 1644 Planarity : 0.006 0.090 1718 Dihedral : 6.110 50.243 1326 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.95 % Allowed : 7.67 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1218 helix: -0.53 (0.22), residues: 512 sheet: -0.96 (0.30), residues: 296 loop : -1.65 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 781 TYR 0.023 0.002 TYR B 584 PHE 0.016 0.002 PHE B 304 TRP 0.011 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (10140) covalent geometry : angle 0.68976 / 0.36 (13788) SS BOND : bond 0.00306 / 0.20 ( 8) SS BOND : angle 1.26027 / 0.76 ( 16) hydrogen bonds : bond 0.06566 / 4.41 ( 478) hydrogen bonds : angle 6.11053 / 4.11 ( 1386) metal coordination : bond 0.00193 / 0.13 ( 6) link_BETA1-4 : bond 0.00656 / 0.43 ( 4) link_BETA1-4 : angle 1.41523 / 0.87 ( 12) link_NAG-ASN : bond 0.00713 / 0.44 ( 10) link_NAG-ASN : angle 4.68606 / 3.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.362 Fit side-chains REVERT: A 161 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 297 MET cc_start: 0.7535 (ptt) cc_final: 0.6812 (ptt) REVERT: A 694 MET cc_start: 0.5931 (mpp) cc_final: 0.5641 (mpp) REVERT: A 728 LEU cc_start: 0.9025 (mt) cc_final: 0.8801 (mt) REVERT: B 61 ARG cc_start: 0.7044 (mpt180) cc_final: 0.6354 (UNCLASSIFIED) REVERT: B 104 GLN cc_start: 0.8862 (pm20) cc_final: 0.8495 (pm20) REVERT: B 161 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 297 MET cc_start: 0.7565 (ptt) cc_final: 0.6827 (ptt) REVERT: B 694 MET cc_start: 0.5947 (mpp) cc_final: 0.5685 (mpp) REVERT: B 728 LEU cc_start: 0.9039 (mt) cc_final: 0.8810 (mt) outliers start: 10 outliers final: 4 residues processed: 143 average time/residue: 0.0796 time to fit residues: 17.0504 Evaluate side-chains 129 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 106 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 74 optimal weight: 0.0270 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN B 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.163498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111906 restraints weight = 13370.004| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.62 r_work: 0.3381 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10168 Z= 0.141 Angle : 0.623 11.215 13846 Z= 0.312 Chirality : 0.046 0.257 1644 Planarity : 0.005 0.082 1718 Dihedral : 5.691 48.296 1326 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.95 % Allowed : 11.46 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1218 helix: 0.12 (0.23), residues: 506 sheet: -0.78 (0.30), residues: 296 loop : -1.64 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.013 0.001 TYR A 486 PHE 0.016 0.001 PHE B 714 TRP 0.011 0.001 TRP A 320 HIS 0.002 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10140) covalent geometry : angle 0.58788 / 0.30 (13788) SS BOND : bond 0.00135 / 0.09 ( 8) SS BOND : angle 0.98642 / 0.59 ( 16) hydrogen bonds : bond 0.05048 / 3.38 ( 478) hydrogen bonds : angle 5.39126 / 3.62 ( 1386) metal coordination : bond 0.00132 / 0.09 ( 6) link_BETA1-4 : bond 0.00727 / 0.49 ( 4) link_BETA1-4 : angle 1.39911 / 0.90 ( 12) link_NAG-ASN : bond 0.00771 / 0.47 ( 10) link_NAG-ASN : angle 4.35459 / 2.87 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6893 (mpt180) cc_final: 0.6545 (mtm-85) REVERT: A 94 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7725 (pp30) REVERT: A 193 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8391 (ttpp) REVERT: A 297 MET cc_start: 0.7389 (ptt) cc_final: 0.6719 (ptt) REVERT: A 728 LEU cc_start: 0.9010 (mt) cc_final: 0.8788 (mt) REVERT: A 779 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 94 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7709 (pp30) REVERT: B 104 GLN cc_start: 0.8835 (pm20) cc_final: 0.8455 (pm20) REVERT: B 193 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8483 (ttpp) REVERT: B 297 MET cc_start: 0.7419 (ptt) cc_final: 0.6723 (ptt) REVERT: B 694 MET cc_start: 0.5903 (mpp) cc_final: 0.5665 (mpp) REVERT: B 728 LEU cc_start: 0.9019 (mt) cc_final: 0.8793 (mt) REVERT: B 779 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8286 (mt-10) outliers start: 10 outliers final: 4 residues processed: 139 average time/residue: 0.0832 time to fit residues: 17.0708 Evaluate side-chains 122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 45 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.164000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110522 restraints weight = 13697.814| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.72 r_work: 0.3354 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10168 Z= 0.159 Angle : 0.618 10.596 13846 Z= 0.307 Chirality : 0.045 0.246 1644 Planarity : 0.004 0.081 1718 Dihedral : 5.534 48.647 1326 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.85 % Allowed : 14.39 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1218 helix: 0.31 (0.23), residues: 514 sheet: -0.70 (0.29), residues: 296 loop : -1.66 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.025 0.001 TYR A 584 PHE 0.012 0.001 PHE A 714 TRP 0.011 0.001 TRP B 320 HIS 0.002 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10140) covalent geometry : angle 0.58556 / 0.30 (13788) SS BOND : bond 0.00137 / 0.09 ( 8) SS BOND : angle 0.99382 / 0.61 ( 16) hydrogen bonds : bond 0.04572 / 3.09 ( 478) hydrogen bonds : angle 5.19719 / 3.49 ( 1386) metal coordination : bond 0.00141 / 0.09 ( 6) link_BETA1-4 : bond 0.00688 / 0.46 ( 4) link_BETA1-4 : angle 1.41878 / 0.92 ( 12) link_NAG-ASN : bond 0.00673 / 0.41 ( 10) link_NAG-ASN : angle 4.15147 / 2.72 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6946 (mpt180) cc_final: 0.6655 (mtm-85) REVERT: A 94 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7655 (pp30) REVERT: A 193 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8701 (mtpp) REVERT: A 297 MET cc_start: 0.7349 (ptt) cc_final: 0.6673 (ptt) REVERT: A 728 LEU cc_start: 0.9066 (mt) cc_final: 0.8855 (mt) REVERT: A 779 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 94 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7637 (pp30) REVERT: B 104 GLN cc_start: 0.8828 (pm20) cc_final: 0.8463 (pm20) REVERT: B 161 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 297 MET cc_start: 0.7348 (ptt) cc_final: 0.6665 (ptt) REVERT: B 728 LEU cc_start: 0.9020 (mt) cc_final: 0.8807 (mt) REVERT: B 779 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8219 (mt-10) outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.0734 time to fit residues: 14.3530 Evaluate side-chains 122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103647 restraints weight = 13746.964| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.77 r_work: 0.3303 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10168 Z= 0.264 Angle : 0.683 9.478 13846 Z= 0.341 Chirality : 0.048 0.250 1644 Planarity : 0.005 0.088 1718 Dihedral : 5.701 50.081 1326 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.08 % Allowed : 16.29 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1218 helix: 0.36 (0.23), residues: 506 sheet: -0.74 (0.29), residues: 296 loop : -1.56 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 100 TYR 0.019 0.002 TYR A 485 PHE 0.024 0.002 PHE A 304 TRP 0.012 0.001 TRP A 320 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (10140) covalent geometry : angle 0.65596 / 0.33 (13788) SS BOND : bond 0.00150 / 0.10 ( 8) SS BOND : angle 1.28698 / 0.79 ( 16) hydrogen bonds : bond 0.04675 / 3.16 ( 478) hydrogen bonds : angle 5.27266 / 3.56 ( 1386) metal coordination : bond 0.00296 / 0.20 ( 6) link_BETA1-4 : bond 0.00666 / 0.43 ( 4) link_BETA1-4 : angle 1.53283 / 1.00 ( 12) link_NAG-ASN : bond 0.00474 / 0.29 ( 10) link_NAG-ASN : angle 3.95364 / 2.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.280 Fit side-chains REVERT: A 61 ARG cc_start: 0.6924 (mpt180) cc_final: 0.6662 (mtm-85) REVERT: A 94 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7755 (pp30) REVERT: A 728 LEU cc_start: 0.9094 (mt) cc_final: 0.8872 (mt) REVERT: B 94 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7756 (pp30) REVERT: B 104 GLN cc_start: 0.8867 (pm20) cc_final: 0.8505 (pm20) REVERT: B 779 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8299 (mt-10) outliers start: 22 outliers final: 14 residues processed: 148 average time/residue: 0.0720 time to fit residues: 16.2926 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 89 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.165455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111411 restraints weight = 13780.355| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.77 r_work: 0.3370 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10168 Z= 0.122 Angle : 0.597 8.766 13846 Z= 0.295 Chirality : 0.044 0.225 1644 Planarity : 0.004 0.076 1718 Dihedral : 5.338 47.668 1326 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.33 % Allowed : 17.14 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1218 helix: 0.59 (0.23), residues: 516 sheet: -0.73 (0.29), residues: 296 loop : -1.69 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.012 0.001 TYR B 173 PHE 0.016 0.001 PHE A 304 TRP 0.009 0.001 TRP A 320 HIS 0.002 0.000 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10140) covalent geometry : angle 0.57293 / 0.29 (13788) SS BOND : bond 0.00127 / 0.08 ( 8) SS BOND : angle 0.82730 / 0.50 ( 16) hydrogen bonds : bond 0.04074 / 2.76 ( 478) hydrogen bonds : angle 5.01956 / 3.38 ( 1386) metal coordination : bond 0.00054 / 0.04 ( 6) link_BETA1-4 : bond 0.00741 / 0.49 ( 4) link_BETA1-4 : angle 1.39639 / 0.91 ( 12) link_NAG-ASN : bond 0.00639 / 0.39 ( 10) link_NAG-ASN : angle 3.56208 / 2.32 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.355 Fit side-chains REVERT: A 61 ARG cc_start: 0.6966 (mpt180) cc_final: 0.6677 (mtm-85) REVERT: A 94 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7650 (pp30) REVERT: A 297 MET cc_start: 0.7483 (ptt) cc_final: 0.6826 (ptt) REVERT: A 761 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: A 779 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8558 (mt-10) REVERT: B 94 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7629 (pp30) REVERT: B 104 GLN cc_start: 0.8810 (pm20) cc_final: 0.8471 (pm20) REVERT: B 297 MET cc_start: 0.7490 (ptt) cc_final: 0.6834 (ptt) REVERT: B 761 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: B 812 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8171 (mp) outliers start: 14 outliers final: 9 residues processed: 135 average time/residue: 0.0697 time to fit residues: 14.4258 Evaluate side-chains 131 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 761 PHE Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110874 restraints weight = 13716.761| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.75 r_work: 0.3364 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10168 Z= 0.143 Angle : 0.600 8.116 13846 Z= 0.296 Chirality : 0.044 0.219 1644 Planarity : 0.004 0.081 1718 Dihedral : 5.218 46.949 1326 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.99 % Allowed : 17.71 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.24), residues: 1218 helix: 0.83 (0.23), residues: 504 sheet: -0.61 (0.29), residues: 296 loop : -1.59 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.013 0.001 TYR B 173 PHE 0.020 0.001 PHE A 304 TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10140) covalent geometry : angle 0.57765 / 0.29 (13788) SS BOND : bond 0.00143 / 0.09 ( 8) SS BOND : angle 0.90331 / 0.55 ( 16) hydrogen bonds : bond 0.03961 / 2.70 ( 478) hydrogen bonds : angle 4.93016 / 3.32 ( 1386) metal coordination : bond 0.00124 / 0.08 ( 6) link_BETA1-4 : bond 0.00688 / 0.46 ( 4) link_BETA1-4 : angle 1.41327 / 0.93 ( 12) link_NAG-ASN : bond 0.00530 / 0.32 ( 10) link_NAG-ASN : angle 3.39506 / 2.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6994 (mpt180) cc_final: 0.6675 (mtm-85) REVERT: A 94 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7688 (pp30) REVERT: A 193 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8709 (mtpp) REVERT: A 297 MET cc_start: 0.7493 (ptt) cc_final: 0.6732 (ptt) REVERT: A 779 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8536 (mt-10) REVERT: A 812 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 94 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7692 (pp30) REVERT: B 297 MET cc_start: 0.7523 (ptt) cc_final: 0.6750 (ptt) REVERT: B 812 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8138 (mp) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.0696 time to fit residues: 14.7036 Evaluate side-chains 137 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.162989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108725 restraints weight = 13681.917| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.76 r_work: 0.3328 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10168 Z= 0.226 Angle : 0.640 7.463 13846 Z= 0.320 Chirality : 0.046 0.222 1644 Planarity : 0.005 0.082 1718 Dihedral : 5.356 48.363 1326 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.18 % Allowed : 17.80 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1218 helix: 0.79 (0.23), residues: 508 sheet: -0.60 (0.29), residues: 296 loop : -1.64 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.023 0.002 TYR B 584 PHE 0.027 0.002 PHE A 304 TRP 0.011 0.001 TRP A 320 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (10140) covalent geometry : angle 0.62042 / 0.32 (13788) SS BOND : bond 0.00152 / 0.10 ( 8) SS BOND : angle 1.10217 / 0.67 ( 16) hydrogen bonds : bond 0.04170 / 2.84 ( 478) hydrogen bonds : angle 5.04210 / 3.41 ( 1386) metal coordination : bond 0.00221 / 0.15 ( 6) link_BETA1-4 : bond 0.00641 / 0.43 ( 4) link_BETA1-4 : angle 1.44480 / 0.95 ( 12) link_NAG-ASN : bond 0.00427 / 0.26 ( 10) link_NAG-ASN : angle 3.27995 / 2.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7062 (mpt180) cc_final: 0.6725 (mtm-85) REVERT: A 94 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: A 193 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8712 (mtpp) REVERT: A 297 MET cc_start: 0.7576 (ptt) cc_final: 0.6804 (ptt) REVERT: A 313 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7776 (tp) REVERT: A 728 LEU cc_start: 0.9167 (mt) cc_final: 0.8861 (pp) REVERT: A 779 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 812 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 61 ARG cc_start: 0.7187 (mpt180) cc_final: 0.6710 (mtm-85) REVERT: B 94 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7751 (pp30) REVERT: B 104 GLN cc_start: 0.8836 (pm20) cc_final: 0.8504 (pm20) REVERT: B 297 MET cc_start: 0.7575 (ptt) cc_final: 0.6802 (ptt) REVERT: B 313 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 812 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8233 (mp) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.0814 time to fit residues: 17.4885 Evaluate side-chains 144 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.164864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110680 restraints weight = 13621.439| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.76 r_work: 0.3353 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10168 Z= 0.150 Angle : 0.607 7.167 13846 Z= 0.301 Chirality : 0.045 0.214 1644 Planarity : 0.004 0.079 1718 Dihedral : 5.235 47.130 1326 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.18 % Allowed : 18.84 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.24), residues: 1218 helix: 0.90 (0.23), residues: 508 sheet: -0.57 (0.29), residues: 296 loop : -1.63 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 781 TYR 0.013 0.001 TYR A 173 PHE 0.023 0.001 PHE A 304 TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10140) covalent geometry : angle 0.58812 / 0.30 (13788) SS BOND : bond 0.00129 / 0.08 ( 8) SS BOND : angle 0.87680 / 0.52 ( 16) hydrogen bonds : bond 0.03971 / 2.72 ( 478) hydrogen bonds : angle 4.95701 / 3.35 ( 1386) metal coordination : bond 0.00138 / 0.09 ( 6) link_BETA1-4 : bond 0.00671 / 0.45 ( 4) link_BETA1-4 : angle 1.41535 / 0.93 ( 12) link_NAG-ASN : bond 0.00496 / 0.30 ( 10) link_NAG-ASN : angle 3.10072 / 2.00 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7064 (mpt180) cc_final: 0.6707 (mtm-85) REVERT: A 94 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7682 (pp30) REVERT: A 193 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8707 (mtpp) REVERT: A 297 MET cc_start: 0.7583 (ptt) cc_final: 0.6806 (ptt) REVERT: A 313 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7835 (tp) REVERT: A 728 LEU cc_start: 0.9153 (mt) cc_final: 0.8842 (pp) REVERT: A 779 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8586 (mt-10) REVERT: A 812 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 61 ARG cc_start: 0.7181 (mpt180) cc_final: 0.6698 (mtm-85) REVERT: B 94 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7684 (pp30) REVERT: B 297 MET cc_start: 0.7543 (ptt) cc_final: 0.6761 (ptt) REVERT: B 313 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7763 (tp) REVERT: B 812 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8201 (mp) outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 0.0836 time to fit residues: 16.7791 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.166227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112335 restraints weight = 13475.176| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.73 r_work: 0.3382 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10168 Z= 0.129 Angle : 0.591 7.039 13846 Z= 0.293 Chirality : 0.044 0.195 1644 Planarity : 0.004 0.078 1718 Dihedral : 5.048 45.466 1326 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.08 % Allowed : 19.22 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1218 helix: 1.19 (0.23), residues: 504 sheet: -0.46 (0.29), residues: 296 loop : -1.53 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 781 TYR 0.013 0.001 TYR A 173 PHE 0.022 0.001 PHE B 714 TRP 0.008 0.001 TRP A 320 HIS 0.002 0.000 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10140) covalent geometry : angle 0.57436 / 0.29 (13788) SS BOND : bond 0.00134 / 0.09 ( 8) SS BOND : angle 0.77036 / 0.46 ( 16) hydrogen bonds : bond 0.03755 / 2.58 ( 478) hydrogen bonds : angle 4.84007 / 3.27 ( 1386) metal coordination : bond 0.00101 / 0.07 ( 6) link_BETA1-4 : bond 0.00725 / 0.49 ( 4) link_BETA1-4 : angle 1.39265 / 0.92 ( 12) link_NAG-ASN : bond 0.00516 / 0.32 ( 10) link_NAG-ASN : angle 2.87620 / 1.85 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6980 (mpt180) cc_final: 0.6640 (mtm-85) REVERT: A 94 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7651 (pp30) REVERT: A 193 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8889 (mtpp) REVERT: A 297 MET cc_start: 0.7531 (ptt) cc_final: 0.6822 (ptt) REVERT: A 313 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7830 (tp) REVERT: B 94 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7646 (pp30) REVERT: B 297 MET cc_start: 0.7532 (ptt) cc_final: 0.6813 (ptt) REVERT: B 812 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8228 (mp) outliers start: 22 outliers final: 11 residues processed: 144 average time/residue: 0.0797 time to fit residues: 17.2345 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.164307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110029 restraints weight = 13702.070| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.75 r_work: 0.3347 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10168 Z= 0.190 Angle : 0.625 6.991 13846 Z= 0.311 Chirality : 0.045 0.203 1644 Planarity : 0.004 0.082 1718 Dihedral : 5.169 46.573 1326 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.61 % Allowed : 19.98 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1218 helix: 1.19 (0.23), residues: 500 sheet: -0.43 (0.29), residues: 296 loop : -1.50 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.016 0.002 TYR B 729 PHE 0.028 0.002 PHE A 304 TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (10140) covalent geometry : angle 0.61005 / 0.31 (13788) SS BOND : bond 0.00146 / 0.09 ( 8) SS BOND : angle 0.99470 / 0.60 ( 16) hydrogen bonds : bond 0.03931 / 2.69 ( 478) hydrogen bonds : angle 4.90283 / 3.31 ( 1386) metal coordination : bond 0.00134 / 0.09 ( 6) link_BETA1-4 : bond 0.00704 / 0.47 ( 4) link_BETA1-4 : angle 1.42597 / 0.94 ( 12) link_NAG-ASN : bond 0.00425 / 0.26 ( 10) link_NAG-ASN : angle 2.85501 / 1.83 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.00 seconds wall clock time: 36 minutes 34.98 seconds (2194.98 seconds total)