Starting phenix.real_space_refine on Sun Dec 29 06:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y63_33632/12_2024/7y63_33632.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y63_33632/12_2024/7y63_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y63_33632/12_2024/7y63_33632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y63_33632/12_2024/7y63_33632.map" model { file = "/net/cci-nas-00/data/ceres_data/7y63_33632/12_2024/7y63_33632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y63_33632/12_2024/7y63_33632.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'ARG:plan': 2, 'TYR:plan': 3} 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, 'ARG:plan': 2, 'TYR:plan': 3} 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 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: 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.26, per 1000 atoms: 0.63 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: 2.96 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 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: 1.11 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: 2.92 Time building geometry restraints manager: 3.33 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 - 23.21: 5690 23.21 - 46.42: 346 46.42 - 69.63: 69 69.63 - 92.83: 25 92.83 - 116.04: 30 Dihedral angle restraints: 6160 sinusoidal: 2526 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 6157 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.450 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 10140 Z= 0.358 Angle : 0.702 7.662 13788 Z= 0.384 Chirality : 0.053 0.519 1644 Planarity : 0.005 0.098 1718 Dihedral : 18.687 116.042 3784 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP B 700 HIS 0.003 0.001 HIS A 492 PHE 0.016 0.002 PHE A 576 TYR 0.018 0.002 TYR A 173 ARG 0.003 0.000 ARG A 785 *********************** 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 : 1.139 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: 0.1995 time to fit residues: 43.9228 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 : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 699 ASN A 774 GLN B 110 GLN B 699 ASN B 774 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10140 Z= 0.245 Angle : 0.702 10.325 13788 Z= 0.352 Chirality : 0.049 0.295 1644 Planarity : 0.005 0.087 1718 Dihedral : 14.864 90.464 1620 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.95 % Allowed : 7.58 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.24), residues: 1218 helix: -0.41 (0.22), residues: 508 sheet: -0.95 (0.30), residues: 296 loop : -1.60 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.014 0.002 PHE A 582 TYR 0.025 0.002 TYR B 584 ARG 0.005 0.000 ARG B 781 *********************** 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 151 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.166 Fit side-chains REVERT: A 104 GLN cc_start: 0.8524 (pm20) cc_final: 0.8227 (pm20) REVERT: A 297 MET cc_start: 0.6860 (ptt) cc_final: 0.6496 (ptt) REVERT: A 694 MET cc_start: 0.5956 (mpp) cc_final: 0.5737 (mpp) REVERT: A 728 LEU cc_start: 0.8876 (mt) cc_final: 0.8651 (mt) REVERT: B 104 GLN cc_start: 0.8515 (pm20) cc_final: 0.8277 (pm20) REVERT: B 297 MET cc_start: 0.6877 (ptt) cc_final: 0.6517 (ptt) REVERT: B 728 LEU cc_start: 0.8891 (mt) cc_final: 0.8683 (mt) outliers start: 10 outliers final: 5 residues processed: 147 average time/residue: 0.1925 time to fit residues: 41.6403 Evaluate side-chains 133 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 61 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 10140 Z= 0.558 Angle : 0.781 11.167 13788 Z= 0.390 Chirality : 0.053 0.287 1644 Planarity : 0.006 0.097 1718 Dihedral : 12.025 69.980 1620 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.52 % Allowed : 14.11 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1218 helix: -0.27 (0.22), residues: 506 sheet: -0.84 (0.30), residues: 296 loop : -1.61 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 320 HIS 0.005 0.002 HIS A 546 PHE 0.020 0.002 PHE B 304 TYR 0.025 0.002 TYR A 485 ARG 0.005 0.001 ARG A 100 *********************** 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 145 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.143 Fit side-chains REVERT: A 61 ARG cc_start: 0.6642 (mpt180) cc_final: 0.6405 (mtm-85) REVERT: A 94 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7708 (pp30) REVERT: A 728 LEU cc_start: 0.8957 (mt) cc_final: 0.8736 (mt) REVERT: A 779 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 61 ARG cc_start: 0.6606 (mpt180) cc_final: 0.6366 (mtm-85) REVERT: B 94 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7697 (pp30) REVERT: B 161 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 728 LEU cc_start: 0.8924 (mt) cc_final: 0.8699 (mt) REVERT: B 779 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7811 (mt-10) outliers start: 16 outliers final: 10 residues processed: 143 average time/residue: 0.1987 time to fit residues: 41.9510 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 574 THR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 788 ILE 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 574 THR Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.1980 chunk 111 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10140 Z= 0.191 Angle : 0.630 10.139 13788 Z= 0.312 Chirality : 0.047 0.267 1644 Planarity : 0.004 0.079 1718 Dihedral : 8.684 58.301 1620 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.14 % Allowed : 16.10 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1218 helix: 0.21 (0.23), residues: 506 sheet: -0.83 (0.29), residues: 296 loop : -1.68 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.002 0.000 HIS B 492 PHE 0.015 0.001 PHE A 130 TYR 0.029 0.001 TYR B 584 ARG 0.004 0.000 ARG B 781 *********************** 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 142 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.023 Fit side-chains REVERT: A 779 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 779 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7716 (mt-10) outliers start: 12 outliers final: 6 residues processed: 140 average time/residue: 0.1947 time to fit residues: 40.1478 Evaluate side-chains 123 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 747 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10140 Z= 0.281 Angle : 0.613 7.817 13788 Z= 0.311 Chirality : 0.046 0.240 1644 Planarity : 0.005 0.087 1718 Dihedral : 7.870 59.878 1620 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.42 % Allowed : 16.76 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1218 helix: 0.39 (0.23), residues: 506 sheet: -0.76 (0.29), residues: 296 loop : -1.65 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.012 0.001 PHE A 130 TYR 0.015 0.001 TYR A 173 ARG 0.003 0.000 ARG B 100 *********************** 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 147 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.100 Fit side-chains REVERT: A 94 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7530 (pp30) REVERT: A 728 LEU cc_start: 0.8945 (mt) cc_final: 0.8737 (pp) REVERT: A 779 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 94 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7527 (pp30) REVERT: B 728 LEU cc_start: 0.8990 (mt) cc_final: 0.8734 (pp) REVERT: B 779 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7732 (mt-10) outliers start: 15 outliers final: 11 residues processed: 142 average time/residue: 0.1900 time to fit residues: 40.1234 Evaluate side-chains 137 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN 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 583 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 747 ILE 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 583 MET Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 747 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 10140 Z= 0.521 Angle : 0.695 7.909 13788 Z= 0.355 Chirality : 0.049 0.247 1644 Planarity : 0.005 0.088 1718 Dihedral : 7.758 57.484 1620 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.22 % Allowed : 17.71 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1218 helix: 0.36 (0.23), residues: 506 sheet: -0.71 (0.30), residues: 296 loop : -1.65 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 320 HIS 0.005 0.001 HIS B 492 PHE 0.025 0.002 PHE A 304 TYR 0.019 0.002 TYR A 485 ARG 0.004 0.001 ARG A 100 *********************** 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 163 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.109 Fit side-chains REVERT: A 94 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7644 (pp30) REVERT: A 812 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 94 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7646 (pp30) REVERT: B 812 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8403 (mp) outliers start: 34 outliers final: 17 residues processed: 155 average time/residue: 0.1928 time to fit residues: 44.1921 Evaluate side-chains 145 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR 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 310 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 38 THR 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 310 LEU 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 812 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10140 Z= 0.176 Angle : 0.581 7.860 13788 Z= 0.297 Chirality : 0.045 0.250 1644 Planarity : 0.004 0.080 1718 Dihedral : 6.962 51.120 1620 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.70 % Allowed : 19.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1218 helix: 0.63 (0.23), residues: 508 sheet: -0.70 (0.29), residues: 296 loop : -1.73 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.002 0.000 HIS B 492 PHE 0.018 0.001 PHE B 714 TYR 0.012 0.001 TYR B 173 ARG 0.003 0.000 ARG B 235 *********************** 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 139 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.108 Fit side-chains REVERT: A 94 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: A 728 LEU cc_start: 0.8932 (mt) cc_final: 0.8723 (pp) REVERT: B 94 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7508 (pp30) outliers start: 18 outliers final: 8 residues processed: 131 average time/residue: 0.1896 time to fit residues: 37.4087 Evaluate side-chains 126 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 709 MET Chi-restraints excluded: chain A residue 712 ASN 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 709 MET Chi-restraints excluded: chain B residue 712 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10140 Z= 0.220 Angle : 0.583 7.697 13788 Z= 0.299 Chirality : 0.044 0.230 1644 Planarity : 0.004 0.083 1718 Dihedral : 6.715 53.403 1620 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.99 % Allowed : 20.08 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1218 helix: 0.88 (0.23), residues: 508 sheet: -0.59 (0.29), residues: 296 loop : -1.73 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS A 492 PHE 0.020 0.001 PHE A 304 TYR 0.014 0.001 TYR A 173 ARG 0.002 0.000 ARG B 61 *********************** 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 144 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.083 Fit side-chains REVERT: A 94 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7503 (pp30) REVERT: A 313 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 521 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7873 (tp) REVERT: A 728 LEU cc_start: 0.8995 (mt) cc_final: 0.8774 (pp) REVERT: B 94 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7500 (pp30) REVERT: B 193 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8477 (mtpp) REVERT: B 313 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7711 (tp) REVERT: B 521 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7853 (tp) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.1963 time to fit residues: 39.9346 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 712 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 0.0270 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10140 Z= 0.274 Angle : 0.593 7.288 13788 Z= 0.304 Chirality : 0.045 0.223 1644 Planarity : 0.004 0.082 1718 Dihedral : 6.581 54.594 1620 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.08 % Allowed : 20.17 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1218 helix: 0.96 (0.23), residues: 508 sheet: -0.56 (0.29), residues: 296 loop : -1.72 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.022 0.001 PHE A 304 TYR 0.016 0.001 TYR B 584 ARG 0.002 0.000 ARG B 61 *********************** 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 144 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.042 Fit side-chains REVERT: A 94 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7547 (pp30) REVERT: A 193 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8485 (mtpp) REVERT: A 313 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7704 (tp) REVERT: A 521 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7885 (tp) REVERT: B 94 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: B 193 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8484 (mtpp) REVERT: B 313 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7713 (tp) REVERT: B 521 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7859 (tp) REVERT: B 527 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7987 (t70) outliers start: 22 outliers final: 12 residues processed: 139 average time/residue: 0.1936 time to fit residues: 39.9850 Evaluate side-chains 138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 712 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10140 Z= 0.167 Angle : 0.563 7.512 13788 Z= 0.288 Chirality : 0.044 0.237 1644 Planarity : 0.004 0.079 1718 Dihedral : 6.085 51.714 1620 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.52 % Allowed : 21.02 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1218 helix: 1.13 (0.23), residues: 508 sheet: -0.48 (0.29), residues: 296 loop : -1.72 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 634 HIS 0.003 0.001 HIS B 492 PHE 0.016 0.001 PHE B 304 TYR 0.012 0.001 TYR A 173 ARG 0.002 0.000 ARG B 85 ********************** 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 153 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.087 Fit side-chains REVERT: A 94 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: A 313 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7753 (tp) REVERT: A 521 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7771 (tp) REVERT: B 61 ARG cc_start: 0.6439 (mtm-85) cc_final: 0.6200 (UNCLASSIFIED) REVERT: B 94 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: B 193 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8538 (mtpp) REVERT: B 313 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7763 (tp) REVERT: B 521 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 527 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7940 (t70) outliers start: 16 outliers final: 7 residues processed: 149 average time/residue: 0.1898 time to fit residues: 41.9838 Evaluate side-chains 137 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 521 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 712 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 14 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.165874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112069 restraints weight = 13701.890| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.77 r_work: 0.3381 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10140 Z= 0.189 Angle : 0.581 8.131 13788 Z= 0.298 Chirality : 0.044 0.230 1644 Planarity : 0.004 0.081 1718 Dihedral : 5.994 53.108 1620 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.80 % Allowed : 21.21 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1218 helix: 1.25 (0.23), residues: 504 sheet: -0.38 (0.29), residues: 296 loop : -1.63 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.003 0.001 HIS B 492 PHE 0.029 0.001 PHE B 714 TYR 0.012 0.001 TYR A 173 ARG 0.002 0.000 ARG B 598 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.52 seconds wall clock time: 37 minutes 57.62 seconds (2277.62 seconds total)