Starting phenix.real_space_refine on Fri Oct 23 09:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oen_70403/10_2026/9oen_70403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oen_70403/10_2026/9oen_70403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oen_70403/10_2026/9oen_70403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oen_70403/10_2026/9oen_70403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oen_70403/10_2026/9oen_70403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oen_70403/10_2026/9oen_70403.map" } resolution = 2.81 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= 0.002 sd= 0.044 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 P 2 5.49 5 S 62 5.16 5 C 5833 2.51 5 N 1528 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9161 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2220 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2252 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2249 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2220 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 38 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: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9161 At special positions: 0 Unit cell: (137.24, 105.28, 74.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 62 16.00 P 2 15.00 O 1734 8.00 N 1528 7.00 C 5833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1002 " - " ASN A 471 " " NAG A1003 " - " ASN A 771 " " NAG B1001 " - " ASN B 886 " " NAG B1002 " - " ASN B 565 " " NAG C1002 " - " ASN C 471 " " NAG C1003 " - " ASN C 771 " " NAG D1001 " - " ASN D 886 " " NAG D1002 " - " ASN D 565 " " NAG E 1 " - " ASN B 549 " " NAG F 1 " - " ASN D 549 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 268.4 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 39.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.851A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 removed outlier: 3.812A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.506A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.885A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.654A pdb=" N HIS B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 614 through 622 Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.531A pdb=" N HIS B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 810 through 818 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 824 through 833 Processing helix chain 'B' and resid 845 through 855 removed outlier: 3.502A pdb=" N ILE B 855 " --> pdb=" O TYR B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 897 removed outlier: 3.670A pdb=" N ILE B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'D' and resid 550 through 562 Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 622 Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 782 through 787 removed outlier: 3.606A pdb=" N HIS D 786 " --> pdb=" O ASP D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 810 removed outlier: 3.532A pdb=" N ASP D 804 " --> pdb=" O SER D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 824 through 833 Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 882 through 897 removed outlier: 4.556A pdb=" N ASN D 886 " --> pdb=" O PRO D 882 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 908 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 710 removed outlier: 3.715A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.915A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.601A pdb=" N GLY A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing sheet with id=AA1, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.817A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLY C 750 " --> pdb=" O VAL C 542 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N VAL C 542 " --> pdb=" O GLY C 750 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU C 752 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ILE C 540 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AA3, first strand: chain 'C' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'B' and resid 527 through 530 removed outlier: 6.843A pdb=" N LEU B 542 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE B 599 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 544 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR B 630 " --> pdb=" O GLY B 876 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY B 876 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B 632 " --> pdb=" O GLY B 874 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 527 through 530 removed outlier: 6.843A pdb=" N LEU B 542 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE B 599 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 544 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR B 630 " --> pdb=" O GLY B 876 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY B 876 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B 632 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N GLY B 865 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N VAL B 657 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ILE B 655 " --> pdb=" O PRO B 867 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA B 869 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 653 " --> pdb=" O ALA B 869 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 649 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY B 795 " --> pdb=" O ILE B 843 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AA7, first strand: chain 'D' and resid 527 through 530 removed outlier: 3.510A pdb=" N TYR D 577 " --> pdb=" O PHE D 527 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU D 542 " --> pdb=" O PHE D 595 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU D 597 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR D 630 " --> pdb=" O GLY D 876 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY D 876 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE D 632 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA D 869 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 653 " --> pdb=" O ALA D 869 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE D 649 " --> pdb=" O TYR D 873 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY D 795 " --> pdb=" O ILE D 843 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N ASP D 845 " --> pdb=" O GLY D 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 643 through 644 removed outlier: 5.967A pdb=" N ALA D 869 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 653 " --> pdb=" O ALA D 869 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE D 649 " --> pdb=" O TYR D 873 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.580A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.580A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLY A 750 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N VAL A 542 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N LEU A 752 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE A 540 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AB4, first strand: chain 'A' and resid 487 through 488 404 hydrogen bonds defined for protein. 1143 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: 1.45 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2293 1.33 - 1.48: 3065 1.48 - 1.64: 3911 1.64 - 1.79: 31 1.79 - 1.94: 69 Bond restraints: 9369 Sorted by residual: bond pdb=" C5 J86 A1001 " pdb=" N3 J86 A1001 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C4 J86 A1001 " pdb=" N2 J86 A1001 " ideal model delta sigma weight residual 1.383 1.484 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C4 J86 C1001 " pdb=" N2 J86 C1001 " ideal model delta sigma weight residual 1.383 1.484 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C5 J86 C1001 " pdb=" N3 J86 C1001 " ideal model delta sigma weight residual 1.384 1.483 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C10 J86 C1001 " pdb=" N2 J86 C1001 " ideal model delta sigma weight residual 1.346 1.420 -0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 9364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 12569 2.99 - 5.98: 106 5.98 - 8.97: 7 8.97 - 11.95: 0 11.95 - 14.94: 4 Bond angle restraints: 12686 Sorted by residual: angle pdb=" C2 J86 C1001 " pdb=" C3 J86 C1001 " pdb=" C7 J86 C1001 " ideal model delta sigma weight residual 120.09 105.15 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C2 J86 A1001 " pdb=" C3 J86 A1001 " pdb=" C7 J86 A1001 " ideal model delta sigma weight residual 120.09 105.34 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C2 J86 C1001 " pdb=" C3 J86 C1001 " pdb=" C4 J86 C1001 " ideal model delta sigma weight residual 121.16 135.15 -13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" C2 J86 A1001 " pdb=" C3 J86 A1001 " pdb=" C4 J86 A1001 " ideal model delta sigma weight residual 121.16 134.94 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" CA LEU B 890 " pdb=" C LEU B 890 " pdb=" O LEU B 890 " ideal model delta sigma weight residual 120.42 117.28 3.14 1.06e+00 8.90e-01 8.80e+00 ... (remaining 12681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 5494 23.35 - 46.70: 222 46.70 - 70.04: 43 70.04 - 93.39: 16 93.39 - 116.74: 7 Dihedral angle restraints: 5782 sinusoidal: 2484 harmonic: 3298 Sorted by residual: dihedral pdb=" C1 NAG B1001 " pdb=" C5 NAG B1001 " pdb=" O5 NAG B1001 " pdb=" C6 NAG B1001 " ideal model delta sinusoidal sigma weight residual 171.16 -72.10 -116.74 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C1 NAG B1001 " pdb=" C5 NAG B1001 " pdb=" O5 NAG B1001 " pdb=" C4 NAG B1001 " ideal model delta sinusoidal sigma weight residual -64.11 52.12 -116.23 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C2 NAG B1001 " pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " pdb=" C5 NAG B1001 " ideal model delta sinusoidal sigma weight residual -62.96 46.92 -109.88 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 5779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1257 0.075 - 0.150: 169 0.150 - 0.225: 2 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 886 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 886 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LEU C 699 " pdb=" N LEU C 699 " pdb=" C LEU C 699 " pdb=" CB LEU C 699 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1427 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " -0.331 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B1001 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " 0.491 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1001 " -0.322 2.00e-02 2.50e+03 2.71e-01 9.19e+02 pdb=" C7 NAG D1001 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D1001 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG D1001 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG D1001 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 451 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 452 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.021 5.00e-02 4.00e+02 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 622 2.73 - 3.27: 8557 3.27 - 3.82: 14724 3.82 - 4.36: 19021 4.36 - 4.90: 32838 Nonbonded interactions: 75762 Sorted by model distance: nonbonded pdb=" O PHE B 792 " pdb=" OH TYR B 816 " model vdw 2.191 3.040 nonbonded pdb=" O ILE A 664 " pdb=" OG1 THR A 749 " model vdw 2.243 3.040 nonbonded pdb=" O ARG D 658 " pdb=" N TYR D 774 " model vdw 2.269 3.120 nonbonded pdb=" O PRO B 878 " pdb=" OG SER B 881 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP D 590 " pdb=" OH TYR D 894 " model vdw 2.358 3.040 ... (remaining 75757 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' and (resid 396 through 416 or (resid 417 and (name N or name CA or na \ me C or name O or name CB )) or resid 418 through 489 or (resid 490 through 495 \ and (name N or name CA or name C or name O or name CB )) or resid 496 through 10 \ 03)) selection = (chain 'C' and (resid 396 through 425 or (resid 426 through 427 and (name N or n \ ame CA or name C or name O or name CB )) or resid 428 or (resid 429 and (name N \ or name CA or name C or name O or name CB )) or resid 430 through 1003)) } ncs_group { reference = (chain 'B' and (resid 513 through 565 or (resid 566 through 567 and (name N or n \ ame CA or name C or name O or name CB )) or resid 568 through 1003)) selection = chain 'D' } ncs_group { reference = 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: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 : 0.007 0.102 9393 Z= 0.291 Angle : 0.749 14.943 12746 Z= 0.357 Chirality : 0.049 0.375 1430 Planarity : 0.011 0.284 1605 Dihedral : 14.523 116.739 3618 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.41 % Allowed : 6.91 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.48 (0.24), residues: 1118 helix: 0.30 (0.25), residues: 436 sheet: -0.66 (0.40), residues: 164 loop : -0.63 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 523 TYR 0.023 0.002 TYR B 579 PHE 0.026 0.003 PHE A 458 TRP 0.008 0.002 TRP A 731 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 ( 9369) covalent geometry : angle 0.73889 / 0.35 (12686) SS BOND : bond 0.00201 / 0.12 ( 12) SS BOND : angle 1.05581 / 0.66 ( 24) hydrogen bonds : bond 0.16665 / 10.85 ( 376) hydrogen bonds : angle 7.77158 / 5.65 ( 1143) link_BETA1-4 : bond 0.00248 / 0.13 ( 2) link_BETA1-4 : angle 2.14378 / 1.11 ( 6) link_NAG-ASN : bond 0.00244 / 0.14 ( 10) link_NAG-ASN : angle 2.36600 / 1.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.362 Fit side-chains REVERT: C 488 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 509 GLN cc_start: 0.8374 (mt0) cc_final: 0.8169 (mt0) REVERT: C 536 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: B 859 CYS cc_start: 0.7437 (m) cc_final: 0.7224 (m) REVERT: D 586 GLN cc_start: 0.8849 (tp40) cc_final: 0.8572 (tp40) REVERT: D 627 MET cc_start: 0.9273 (ttp) cc_final: 0.9038 (ttm) REVERT: D 799 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8656 (mt-10) REVERT: D 871 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8612 (mt-10) REVERT: D 909 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7669 (mttp) REVERT: A 668 ASN cc_start: 0.8625 (m-40) cc_final: 0.8408 (m-40) REVERT: A 707 GLU cc_start: 0.7375 (tt0) cc_final: 0.7138 (tt0) outliers start: 4 outliers final: 0 residues processed: 144 average time/residue: 0.6888 time to fit residues: 104.8057 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 536 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 440 ASN C 509 GLN C 521 ASN B 808 GLN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN A 696 GLN A 724 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118890 restraints weight = 8543.856| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.78 r_work: 0.3249 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9393 Z= 0.144 Angle : 0.563 11.224 12746 Z= 0.288 Chirality : 0.045 0.234 1430 Planarity : 0.004 0.049 1605 Dihedral : 10.016 82.871 1511 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.96 % Allowed : 9.60 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.07 (0.25), residues: 1118 helix: 0.72 (0.25), residues: 434 sheet: -0.42 (0.42), residues: 154 loop : -0.48 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 807 TYR 0.019 0.001 TYR B 579 PHE 0.023 0.002 PHE B 527 TRP 0.007 0.001 TRP C 731 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 9369) covalent geometry : angle 0.55536 / 0.29 (12686) SS BOND : bond 0.00195 / 0.13 ( 12) SS BOND : angle 0.71763 / 0.46 ( 24) hydrogen bonds : bond 0.04371 / 2.82 ( 376) hydrogen bonds : angle 5.67851 / 4.18 ( 1143) link_BETA1-4 : bond 0.00332 / 0.17 ( 2) link_BETA1-4 : angle 2.04288 / 1.11 ( 6) link_NAG-ASN : bond 0.00425 / 0.24 ( 10) link_NAG-ASN : angle 1.78402 / 1.09 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 488 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6956 (mm-30) REVERT: C 497 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7378 (pt0) REVERT: C 536 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8840 (pt0) REVERT: B 589 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: B 859 CYS cc_start: 0.7659 (m) cc_final: 0.7450 (m) REVERT: D 586 GLN cc_start: 0.8828 (tp40) cc_final: 0.8604 (tp40) REVERT: D 627 MET cc_start: 0.8925 (ttp) cc_final: 0.8717 (ttm) REVERT: D 803 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: A 471 ASN cc_start: 0.8213 (t0) cc_final: 0.7959 (t0) REVERT: A 668 ASN cc_start: 0.8592 (m-40) cc_final: 0.8316 (m-40) REVERT: A 707 GLU cc_start: 0.7466 (tt0) cc_final: 0.7224 (tt0) outliers start: 19 outliers final: 5 residues processed: 141 average time/residue: 0.6205 time to fit residues: 92.9464 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [24, 29, 76, 40, 23, 105, 4, 6, 0, 25, 12] chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119717 restraints weight = 8567.625| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.79 r_work: 0.3259 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9393 Z= 0.135 Angle : 0.535 10.346 12746 Z= 0.273 Chirality : 0.043 0.198 1430 Planarity : 0.004 0.051 1605 Dihedral : 8.728 79.951 1511 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.37 % Allowed : 9.70 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.02 (0.25), residues: 1118 helix: 0.82 (0.25), residues: 440 sheet: -0.31 (0.42), residues: 154 loop : -0.49 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 819 TYR 0.017 0.001 TYR B 579 PHE 0.023 0.002 PHE B 527 TRP 0.007 0.001 TRP C 731 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9369) covalent geometry : angle 0.52895 / 0.27 (12686) SS BOND : bond 0.00150 / 0.10 ( 12) SS BOND : angle 0.85285 / 0.53 ( 24) hydrogen bonds : bond 0.03962 / 2.57 ( 376) hydrogen bonds : angle 5.35938 / 3.96 ( 1143) link_BETA1-4 : bond 0.00442 / 0.23 ( 2) link_BETA1-4 : angle 1.84478 / 1.02 ( 6) link_NAG-ASN : bond 0.00269 / 0.14 ( 10) link_NAG-ASN : angle 1.49350 / 0.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: C 488 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 589 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: B 859 CYS cc_start: 0.7587 (m) cc_final: 0.7354 (m) REVERT: B 885 SER cc_start: 0.8347 (t) cc_final: 0.8020 (p) REVERT: D 586 GLN cc_start: 0.8851 (tp40) cc_final: 0.8544 (tp40) REVERT: D 799 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8547 (mt-10) REVERT: D 803 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: D 871 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8530 (mt-10) REVERT: D 909 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7981 (ttmt) REVERT: A 471 ASN cc_start: 0.8194 (t0) cc_final: 0.7801 (t0) REVERT: A 528 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: A 668 ASN cc_start: 0.8596 (m-40) cc_final: 0.8329 (m-40) REVERT: A 677 ASP cc_start: 0.7308 (t0) cc_final: 0.7080 (t0) REVERT: A 707 GLU cc_start: 0.7455 (tt0) cc_final: 0.7219 (tt0) outliers start: 23 outliers final: 8 residues processed: 142 average time/residue: 0.6527 time to fit residues: 98.0192 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [46, 48, 23, 51, 32, 79, 93, 19, 5, 110, 86] chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 674 ASN A 705 HIS A 724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121490 restraints weight = 8710.100| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.80 r_work: 0.3282 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9393 Z= 0.101 Angle : 0.484 11.313 12746 Z= 0.249 Chirality : 0.042 0.181 1430 Planarity : 0.004 0.050 1605 Dihedral : 7.771 79.897 1511 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.37 % Allowed : 10.63 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.19 (0.25), residues: 1118 helix: 0.98 (0.25), residues: 442 sheet: -0.33 (0.41), residues: 156 loop : -0.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 819 TYR 0.014 0.001 TYR B 579 PHE 0.020 0.001 PHE B 527 TRP 0.006 0.001 TRP C 498 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 9369) covalent geometry : angle 0.47746 / 0.25 (12686) SS BOND : bond 0.00139 / 0.09 ( 12) SS BOND : angle 0.72439 / 0.45 ( 24) hydrogen bonds : bond 0.03306 / 2.15 ( 376) hydrogen bonds : angle 5.06150 / 3.76 ( 1143) link_BETA1-4 : bond 0.00416 / 0.21 ( 2) link_BETA1-4 : angle 1.69651 / 0.95 ( 6) link_NAG-ASN : bond 0.00287 / 0.16 ( 10) link_NAG-ASN : angle 1.50371 / 1.01 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7639 (mmp) cc_final: 0.7273 (mtt) REVERT: C 488 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 859 CYS cc_start: 0.7508 (m) cc_final: 0.7248 (m) REVERT: B 885 SER cc_start: 0.8293 (t) cc_final: 0.8058 (p) REVERT: D 586 GLN cc_start: 0.8855 (tp40) cc_final: 0.8564 (tp40) REVERT: D 803 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: A 471 ASN cc_start: 0.8130 (t0) cc_final: 0.7762 (t0) REVERT: A 668 ASN cc_start: 0.8606 (m-40) cc_final: 0.8339 (m-40) REVERT: A 677 ASP cc_start: 0.7310 (t0) cc_final: 0.7060 (t0) REVERT: A 681 TYR cc_start: 0.9215 (p90) cc_final: 0.8980 (p90) REVERT: A 707 GLU cc_start: 0.7417 (tt0) cc_final: 0.7200 (tt0) outliers start: 23 outliers final: 7 residues processed: 141 average time/residue: 0.5877 time to fit residues: 88.0649 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [102, 69, 103, 55, 106, 66, 78, 65, 108, 16, 17] chunk 102 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 65 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127796 restraints weight = 8348.684| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.74 r_work: 0.3320 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9393 Z= 0.159 Angle : 0.549 10.927 12746 Z= 0.278 Chirality : 0.044 0.181 1430 Planarity : 0.004 0.053 1605 Dihedral : 7.225 77.137 1508 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.48 % Allowed : 11.56 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.13 (0.25), residues: 1118 helix: 0.89 (0.25), residues: 442 sheet: -0.32 (0.41), residues: 154 loop : -0.39 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 819 TYR 0.019 0.002 TYR B 579 PHE 0.025 0.002 PHE B 527 TRP 0.008 0.001 TRP C 731 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 9369) covalent geometry : angle 0.53837 / 0.28 (12686) SS BOND : bond 0.00203 / 0.12 ( 12) SS BOND : angle 1.08099 / 0.68 ( 24) hydrogen bonds : bond 0.03953 / 2.55 ( 376) hydrogen bonds : angle 5.15554 / 3.82 ( 1143) link_BETA1-4 : bond 0.00350 / 0.18 ( 2) link_BETA1-4 : angle 1.77712 / 0.99 ( 6) link_NAG-ASN : bond 0.00302 / 0.18 ( 10) link_NAG-ASN : angle 1.99341 / 1.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7744 (mmp) cc_final: 0.7349 (mtt) REVERT: C 488 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7065 (mm-30) REVERT: C 536 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8554 (pt0) REVERT: C 699 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 859 CYS cc_start: 0.7545 (m) cc_final: 0.7274 (m) REVERT: B 885 SER cc_start: 0.8387 (t) cc_final: 0.8094 (p) REVERT: D 586 GLN cc_start: 0.8879 (tp40) cc_final: 0.8598 (tp40) REVERT: D 799 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8484 (mt-10) REVERT: D 803 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: D 815 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: D 871 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8546 (mt-10) REVERT: D 909 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7809 (mttp) REVERT: A 471 ASN cc_start: 0.8248 (t0) cc_final: 0.7871 (t0) REVERT: A 528 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: A 668 ASN cc_start: 0.8612 (m-40) cc_final: 0.8357 (m-40) REVERT: A 677 ASP cc_start: 0.7452 (t0) cc_final: 0.7150 (t0) REVERT: A 707 GLU cc_start: 0.7408 (tt0) cc_final: 0.7187 (tt0) outliers start: 24 outliers final: 10 residues processed: 136 average time/residue: 0.6123 time to fit residues: 88.5089 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [26, 34, 81, 93, 46, 89, 109, 31, 7, 87, 97] chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN A 509 GLN A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120867 restraints weight = 8713.333| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.80 r_work: 0.3278 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9393 Z= 0.111 Angle : 0.490 9.428 12746 Z= 0.252 Chirality : 0.042 0.178 1430 Planarity : 0.004 0.051 1605 Dihedral : 6.889 78.839 1508 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.06 % Allowed : 12.38 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.24 (0.25), residues: 1118 helix: 1.01 (0.25), residues: 442 sheet: -0.34 (0.41), residues: 156 loop : -0.32 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 819 TYR 0.016 0.001 TYR B 579 PHE 0.021 0.001 PHE B 527 TRP 0.006 0.001 TRP C 498 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9369) covalent geometry : angle 0.47883 / 0.25 (12686) SS BOND : bond 0.00175 / 0.11 ( 12) SS BOND : angle 0.76986 / 0.48 ( 24) hydrogen bonds : bond 0.03345 / 2.18 ( 376) hydrogen bonds : angle 5.02552 / 3.73 ( 1143) link_BETA1-4 : bond 0.00400 / 0.20 ( 2) link_BETA1-4 : angle 1.73569 / 0.97 ( 6) link_NAG-ASN : bond 0.00316 / 0.18 ( 10) link_NAG-ASN : angle 2.03401 / 1.43 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7648 (mmp) cc_final: 0.7283 (mtt) REVERT: C 488 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7006 (mm-30) REVERT: B 859 CYS cc_start: 0.7476 (m) cc_final: 0.7224 (m) REVERT: B 885 SER cc_start: 0.8320 (t) cc_final: 0.8095 (p) REVERT: D 586 GLN cc_start: 0.8860 (tp40) cc_final: 0.8578 (tp40) REVERT: D 803 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: D 815 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 471 ASN cc_start: 0.8067 (t0) cc_final: 0.7695 (t0) REVERT: A 528 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: A 668 ASN cc_start: 0.8561 (m-40) cc_final: 0.8294 (m-40) REVERT: A 673 ARG cc_start: 0.8047 (mmt90) cc_final: 0.7758 (mmt180) REVERT: A 677 ASP cc_start: 0.7379 (t0) cc_final: 0.7076 (t0) outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 0.6072 time to fit residues: 89.0851 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [33, 17, 111, 52, 99, 23, 89, 22, 75, 87, 9] chunk 33 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129660 restraints weight = 8401.859| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.73 r_work: 0.3346 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9393 Z= 0.115 Angle : 0.493 7.889 12746 Z= 0.255 Chirality : 0.042 0.177 1430 Planarity : 0.004 0.051 1605 Dihedral : 6.757 78.363 1508 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.96 % Allowed : 13.11 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.27 (0.25), residues: 1118 helix: 1.05 (0.25), residues: 442 sheet: -0.39 (0.41), residues: 156 loop : -0.30 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 819 TYR 0.015 0.001 TYR B 579 PHE 0.021 0.002 PHE B 527 TRP 0.007 0.001 TRP C 768 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 ( 9369) covalent geometry : angle 0.48251 / 0.25 (12686) SS BOND : bond 0.00209 / 0.12 ( 12) SS BOND : angle 1.05011 / 0.64 ( 24) hydrogen bonds : bond 0.03357 / 2.18 ( 376) hydrogen bonds : angle 4.97713 / 3.70 ( 1143) link_BETA1-4 : bond 0.00375 / 0.19 ( 2) link_BETA1-4 : angle 1.72679 / 0.96 ( 6) link_NAG-ASN : bond 0.00290 / 0.17 ( 10) link_NAG-ASN : angle 1.80068 / 1.25 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7703 (mmp) cc_final: 0.7350 (mtt) REVERT: C 488 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7031 (mm-30) REVERT: C 536 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: B 859 CYS cc_start: 0.7514 (m) cc_final: 0.7258 (m) REVERT: B 885 SER cc_start: 0.8347 (t) cc_final: 0.8126 (p) REVERT: D 586 GLN cc_start: 0.8849 (tp40) cc_final: 0.8563 (tp40) REVERT: D 799 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8495 (mt-10) REVERT: D 803 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: D 815 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: D 871 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8566 (mt-10) REVERT: D 909 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7679 (mttp) REVERT: A 471 ASN cc_start: 0.8089 (t0) cc_final: 0.7728 (t0) REVERT: A 528 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: A 668 ASN cc_start: 0.8596 (m-40) cc_final: 0.8341 (m-40) REVERT: A 673 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7779 (mmt180) REVERT: A 677 ASP cc_start: 0.7453 (t0) cc_final: 0.7134 (t0) outliers start: 19 outliers final: 12 residues processed: 137 average time/residue: 0.6105 time to fit residues: 88.8989 Evaluate side-chains 141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [78, 60, 95, 102, 53, 28, 15, 46, 94, 18, 98] chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128769 restraints weight = 8353.822| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.74 r_work: 0.3338 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9393 Z= 0.134 Angle : 0.507 6.321 12746 Z= 0.263 Chirality : 0.043 0.177 1430 Planarity : 0.004 0.051 1605 Dihedral : 6.725 77.552 1508 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.37 % Allowed : 12.90 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.25 (0.25), residues: 1118 helix: 1.00 (0.25), residues: 442 sheet: -0.36 (0.41), residues: 154 loop : -0.30 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 819 TYR 0.017 0.001 TYR B 579 PHE 0.023 0.002 PHE B 527 TRP 0.007 0.001 TRP C 768 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 9369) covalent geometry : angle 0.49910 / 0.26 (12686) SS BOND : bond 0.00206 / 0.12 ( 12) SS BOND : angle 1.08285 / 0.66 ( 24) hydrogen bonds : bond 0.03556 / 2.31 ( 376) hydrogen bonds : angle 5.02454 / 3.73 ( 1143) link_BETA1-4 : bond 0.00409 / 0.21 ( 2) link_BETA1-4 : angle 1.77363 / 0.98 ( 6) link_NAG-ASN : bond 0.00251 / 0.14 ( 10) link_NAG-ASN : angle 1.50322 / 1.01 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7710 (mmp) cc_final: 0.7352 (mtt) REVERT: C 488 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 536 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: B 859 CYS cc_start: 0.7518 (m) cc_final: 0.7267 (m) REVERT: B 885 SER cc_start: 0.8395 (t) cc_final: 0.8145 (p) REVERT: D 586 GLN cc_start: 0.8880 (tp40) cc_final: 0.8601 (tp40) REVERT: D 799 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8526 (mt-10) REVERT: D 803 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: D 815 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: D 871 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 399 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7906 (mtpp) REVERT: A 471 ASN cc_start: 0.8113 (t0) cc_final: 0.7752 (t0) REVERT: A 504 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 528 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: A 668 ASN cc_start: 0.8606 (m-40) cc_final: 0.8372 (m-40) REVERT: A 673 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7783 (mmt180) REVERT: A 677 ASP cc_start: 0.7502 (t0) cc_final: 0.7155 (t0) outliers start: 23 outliers final: 10 residues processed: 140 average time/residue: 0.6250 time to fit residues: 92.7990 Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [67, 6, 110, 26, 57, 91, 36, 86, 97, 14, 37] chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127406 restraints weight = 8385.914| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.73 r_work: 0.3318 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9393 Z= 0.171 Angle : 0.552 6.530 12746 Z= 0.285 Chirality : 0.044 0.178 1430 Planarity : 0.004 0.052 1605 Dihedral : 6.805 76.955 1508 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.86 % Allowed : 13.62 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.14 (0.25), residues: 1118 helix: 0.90 (0.25), residues: 440 sheet: -0.40 (0.41), residues: 154 loop : -0.35 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 819 TYR 0.019 0.002 TYR B 579 PHE 0.026 0.002 PHE B 527 TRP 0.009 0.001 TRP C 768 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 ( 9369) covalent geometry : angle 0.54571 / 0.28 (12686) SS BOND : bond 0.00189 / 0.12 ( 12) SS BOND : angle 1.12851 / 0.71 ( 24) hydrogen bonds : bond 0.04012 / 2.60 ( 376) hydrogen bonds : angle 5.14656 / 3.81 ( 1143) link_BETA1-4 : bond 0.00349 / 0.18 ( 2) link_BETA1-4 : angle 1.88774 / 1.03 ( 6) link_NAG-ASN : bond 0.00227 / 0.13 ( 10) link_NAG-ASN : angle 1.38502 / 0.89 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7742 (mmp) cc_final: 0.7347 (mtt) REVERT: C 536 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: B 859 CYS cc_start: 0.7624 (m) cc_final: 0.7385 (m) REVERT: B 885 SER cc_start: 0.8434 (t) cc_final: 0.8136 (p) REVERT: D 586 GLN cc_start: 0.8887 (tp40) cc_final: 0.8614 (tp40) REVERT: D 799 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8524 (mt-10) REVERT: D 803 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: D 815 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: D 871 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8612 (mt-10) REVERT: D 909 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7730 (mttp) REVERT: A 399 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7922 (mtpp) REVERT: A 471 ASN cc_start: 0.8121 (t0) cc_final: 0.7757 (t0) REVERT: A 497 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7702 (mm-30) REVERT: A 528 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: A 677 ASP cc_start: 0.7585 (t0) cc_final: 0.7222 (t0) outliers start: 18 outliers final: 10 residues processed: 141 average time/residue: 0.6138 time to fit residues: 91.8209 Evaluate side-chains 141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [11, 46, 28, 8, 29, 39, 74, 42, 102, 71, 37] chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 808 GLN A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129312 restraints weight = 8410.582| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.73 r_work: 0.3344 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9393 Z= 0.111 Angle : 0.490 6.346 12746 Z= 0.256 Chirality : 0.042 0.177 1430 Planarity : 0.004 0.050 1605 Dihedral : 6.699 78.717 1508 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.65 % Allowed : 14.04 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.27 (0.25), residues: 1118 helix: 1.03 (0.25), residues: 442 sheet: -0.40 (0.41), residues: 156 loop : -0.28 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 819 TYR 0.016 0.001 TYR B 579 PHE 0.021 0.001 PHE B 527 TRP 0.008 0.001 TRP C 768 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9369) covalent geometry : angle 0.48479 / 0.26 (12686) SS BOND : bond 0.00149 / 0.10 ( 12) SS BOND : angle 0.88067 / 0.54 ( 24) hydrogen bonds : bond 0.03328 / 2.17 ( 376) hydrogen bonds : angle 4.99894 / 3.71 ( 1143) link_BETA1-4 : bond 0.00425 / 0.21 ( 2) link_BETA1-4 : angle 1.81738 / 1.00 ( 6) link_NAG-ASN : bond 0.00258 / 0.14 ( 10) link_NAG-ASN : angle 1.23542 / 0.81 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: C 415 MET cc_start: 0.7698 (mmp) cc_final: 0.7335 (mtt) REVERT: C 536 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8513 (pt0) REVERT: B 859 CYS cc_start: 0.7494 (m) cc_final: 0.7243 (m) REVERT: B 885 SER cc_start: 0.8403 (t) cc_final: 0.8159 (p) REVERT: D 586 GLN cc_start: 0.8845 (tp40) cc_final: 0.8583 (tp40) REVERT: D 799 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8526 (mt-10) REVERT: D 803 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: D 815 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: D 871 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 399 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7875 (mtpp) REVERT: A 471 ASN cc_start: 0.8052 (t0) cc_final: 0.7711 (t0) REVERT: A 673 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7799 (mmt180) REVERT: A 677 ASP cc_start: 0.7566 (t0) cc_final: 0.7206 (t0) outliers start: 16 outliers final: 10 residues processed: 142 average time/residue: 0.5924 time to fit residues: 89.5207 Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 801 SER Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 751 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [36, 102, 78, 39, 44, 43, 14, 70, 76, 16, 79] chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 ASN A 674 ASN A 724 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127249 restraints weight = 8273.856| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.72 r_work: 0.3314 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9393 Z= 0.181 Angle : 0.560 6.737 12746 Z= 0.289 Chirality : 0.045 0.179 1430 Planarity : 0.004 0.052 1605 Dihedral : 6.788 76.874 1508 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.65 % Allowed : 14.14 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.10 (0.25), residues: 1118 helix: 0.84 (0.25), residues: 442 sheet: -0.41 (0.41), residues: 154 loop : -0.35 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 819 TYR 0.020 0.002 TYR B 579 PHE 0.026 0.002 PHE B 527 TRP 0.007 0.001 TRP C 731 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 ( 9369) covalent geometry : angle 0.55377 / 0.29 (12686) SS BOND : bond 0.00203 / 0.13 ( 12) SS BOND : angle 1.08709 / 0.69 ( 24) hydrogen bonds : bond 0.04076 / 2.63 ( 376) hydrogen bonds : angle 5.15714 / 3.81 ( 1143) link_BETA1-4 : bond 0.00358 / 0.18 ( 2) link_BETA1-4 : angle 1.92455 / 1.04 ( 6) link_NAG-ASN : bond 0.00231 / 0.13 ( 10) link_NAG-ASN : angle 1.29250 / 0.81 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3133.29 seconds wall clock time: 54 minutes 4.80 seconds (3244.80 seconds total)