Starting phenix.real_space_refine on Fri Sep 19 00:10:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqp_20450/09_2025/6pqp_20450.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqp_20450/09_2025/6pqp_20450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2025/6pqp_20450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2025/6pqp_20450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2025/6pqp_20450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2025/6pqp_20450.map" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 152 5.16 5 C 13524 2.51 5 N 3216 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20492 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 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: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'6OU': 5, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'6OU': 1, 'LBN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'6OU': 5, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 282 Unusual residues: {'6OU': 6, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: D, F, G, H Time building chain proxies: 6.61, per 1000 atoms: 0.32 Number of scatterers: 20492 At special positions: 0 Unit cell: (111.93, 111.93, 148.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 24 15.00 O 3576 8.00 N 3216 7.00 C 13524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 462 " distance=0.00 Simple disulfide: pdb=" SG CYS D 540 " - pdb=" SG CYS D 540 " distance=0.00 Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 608 " distance=0.00 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 621 " distance=0.00 Simple disulfide: pdb=" SG CYS D 633 " - pdb=" SG CYS D 633 " distance=0.00 Simple disulfide: pdb=" SG CYS D 641 " - pdb=" SG CYS D 641 " distance=0.00 Simple disulfide: pdb=" SG CYS D 651 " - pdb=" SG CYS D 651 " distance=0.00 Simple disulfide: pdb=" SG CYS D 665 " - pdb=" SG CYS D 665 " distance=0.00 Simple disulfide: pdb=" SG CYS D 703 " - pdb=" SG CYS D 703 " distance=0.00 Simple disulfide: pdb=" SG CYS D 727 " - pdb=" SG CYS D 727 " distance=0.00 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 773 " distance=0.00 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 786 " distance=0.00 Simple disulfide: pdb=" SG CYS D 834 " - pdb=" SG CYS D 834 " distance=0.00 Simple disulfide: pdb=" SG CYS D 856 " - pdb=" SG CYS D 856 " distance=0.00 Simple disulfide: pdb=" SG CYS D1021 " - pdb=" SG CYS D1021 " distance=0.00 Simple disulfide: pdb=" SG CYS D1025 " - pdb=" SG CYS D1025 " distance=0.00 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=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN D 747 " " NAG G 1 " - " ASN B 747 " " NAG H 1 " - " ASN C 747 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 877.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 8 sheets defined 73.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.513A pdb=" N TYR A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.525A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR A 670 " --> pdb=" O PRO A 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 671' Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.584A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.801A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.586A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 846 removed outlier: 3.687A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER A 899 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.512A pdb=" N TYR D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.524A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 3.766A pdb=" N THR D 670 " --> pdb=" O PRO D 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 666 through 671' Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 683 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 removed outlier: 3.584A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.802A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 796 removed outlier: 3.586A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.760A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 846 removed outlier: 3.687A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN D 851 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER D 899 " --> pdb=" O ASP D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 928 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 Processing helix chain 'D' and resid 1016 through 1024 Processing helix chain 'D' and resid 1040 through 1072 Processing helix chain 'B' and resid 447 through 456 removed outlier: 3.513A pdb=" N TYR B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.524A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.612A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.853A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 671' Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 removed outlier: 3.583A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.802A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 796 removed outlier: 3.586A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 846 removed outlier: 3.687A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE B 877 " --> pdb=" O SER B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER B 899 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.987A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 Processing helix chain 'B' and resid 1016 through 1024 Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.513A pdb=" N TYR C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.525A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR C 670 " --> pdb=" O PRO C 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 666 through 671' Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 683 through 692 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 removed outlier: 3.583A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.801A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 796 removed outlier: 3.587A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 846 removed outlier: 3.686A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN C 851 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE C 877 " --> pdb=" O SER C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.613A pdb=" N SER C 899 " --> pdb=" O ASP C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1016 through 1024 Processing helix chain 'C' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 656 through 659 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 656 through 659 Processing sheet with id=AA4, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 656 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 656 through 659 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3471 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: 3.34 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3064 1.30 - 1.43: 5374 1.43 - 1.56: 11947 1.56 - 1.68: 255 1.68 - 1.81: 276 Bond restraints: 20916 Sorted by residual: bond pdb=" O2 LBN C1208 " pdb=" P1 LBN C1208 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2 LBN A1206 " pdb=" P1 LBN A1206 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2 LBN D1205 " pdb=" P1 LBN D1205 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O2 LBN B1207 " pdb=" P1 LBN B1207 " ideal model delta sigma weight residual 1.650 1.796 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O22 6OU B1204 " pdb=" P23 6OU B1204 " ideal model delta sigma weight residual 1.643 1.738 -0.095 2.00e-02 2.50e+03 2.26e+01 ... (remaining 20911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 27152 3.07 - 6.14: 848 6.14 - 9.20: 120 9.20 - 12.27: 35 12.27 - 15.34: 13 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 108.23 119.24 -11.01 1.53e+00 4.27e-01 5.18e+01 angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 108.23 119.22 -10.99 1.53e+00 4.27e-01 5.16e+01 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 108.23 119.20 -10.97 1.53e+00 4.27e-01 5.14e+01 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 108.23 119.17 -10.94 1.53e+00 4.27e-01 5.11e+01 angle pdb=" O22 6OU D1204 " pdb=" P23 6OU D1204 " pdb=" O26 6OU D1204 " ideal model delta sigma weight residual 93.95 109.29 -15.34 3.00e+00 1.11e-01 2.61e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 12192 34.20 - 68.39: 420 68.39 - 102.59: 168 102.59 - 136.78: 32 136.78 - 170.98: 32 Dihedral angle restraints: 12844 sinusoidal: 5600 harmonic: 7244 Sorted by residual: dihedral pdb=" CB CYS D 462 " pdb=" SG CYS D 462 " pdb=" SG CYS D 462 " pdb=" CB CYS D 462 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS D 540 " pdb=" SG CYS D 540 " pdb=" SG CYS D 540 " pdb=" CB CYS D 540 " ideal model delta sinusoidal sigma weight residual 147.25 90.57 56.68 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" CB CYS D 608 " pdb=" SG CYS D 608 " pdb=" SG CYS D 608 " pdb=" CB CYS D 608 " ideal model delta sinusoidal sigma weight residual 119.20 0.00 119.20 1 1.00e+01 1.00e-02 1.43e+02 ... (remaining 12841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 3220 1.215 - 2.431: 0 2.431 - 3.646: 0 3.646 - 4.861: 0 4.861 - 6.076: 4 Chirality restraints: 3224 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 747 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 3.68 -6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 747 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 3.68 -6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 747 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 3.67 -6.07 2.00e-01 2.50e+01 9.23e+02 ... (remaining 3221 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.234 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG H 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.234 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG E 2 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.234 2.00e-02 2.50e+03 1.95e-01 4.73e+02 pdb=" C7 NAG F 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 347 2.69 - 3.24: 18481 3.24 - 3.79: 30503 3.79 - 4.35: 40445 4.35 - 4.90: 66550 Nonbonded interactions: 156326 Sorted by model distance: nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.132 3.120 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.284 3.040 ... (remaining 156321 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 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'B' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'C' and (resid 446 through 1079 or resid 1204)) selection = (chain 'D' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.630 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.014 0.451 20928 Z= 0.635 Angle : 1.388 35.721 28208 Z= 0.611 Chirality : 0.226 6.076 3224 Planarity : 0.011 0.195 3392 Dihedral : 21.817 170.977 8108 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.19 % Allowed : 4.80 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.28 (0.14), residues: 2436 helix: -2.21 (0.09), residues: 1756 sheet: 1.02 (0.80), residues: 68 loop : -1.74 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 919 TYR 0.042 0.003 TYR C 785 PHE 0.035 0.004 PHE D 888 TRP 0.050 0.003 TRP B 515 HIS 0.011 0.003 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.01199 (20916) covalent geometry : angle 1.29170 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.14840 ( 1173) hydrogen bonds : angle 6.08031 ( 3471) Misc. bond : bond 0.02139 ( 4) link_BETA1-4 : bond 0.00041 ( 4) link_BETA1-4 : angle 0.04874 ( 12) link_NAG-ASN : bond 0.45049 ( 4) link_NAG-ASN : angle 24.68929 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 614 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 720 MET cc_start: 0.7790 (mmm) cc_final: 0.7513 (mmm) REVERT: A 826 ILE cc_start: 0.8749 (mt) cc_final: 0.8521 (tt) REVERT: A 930 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 1042 MET cc_start: 0.7688 (ppp) cc_final: 0.7398 (ptt) REVERT: D 571 ASN cc_start: 0.8297 (m110) cc_final: 0.7993 (t0) REVERT: D 783 PHE cc_start: 0.8045 (m-80) cc_final: 0.7789 (m-10) REVERT: D 981 GLU cc_start: 0.8048 (tp30) cc_final: 0.7732 (mm-30) REVERT: D 986 LEU cc_start: 0.9266 (tt) cc_final: 0.8922 (tt) REVERT: D 1077 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 591 LYS cc_start: 0.9374 (mttt) cc_final: 0.9169 (mtmm) REVERT: B 643 LEU cc_start: 0.7727 (mp) cc_final: 0.7335 (mp) REVERT: B 1075 ILE cc_start: 0.7807 (mt) cc_final: 0.7078 (mm) REVERT: C 770 ILE cc_start: 0.9317 (mt) cc_final: 0.9084 (mm) REVERT: C 981 GLU cc_start: 0.7936 (tp30) cc_final: 0.7619 (tp30) REVERT: C 985 SER cc_start: 0.9199 (t) cc_final: 0.8779 (p) REVERT: C 1075 ILE cc_start: 0.8628 (mt) cc_final: 0.8006 (mm) outliers start: 4 outliers final: 3 residues processed: 614 average time/residue: 0.1332 time to fit residues: 125.0935 Evaluate side-chains 308 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 305 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain B residue 611 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 549 ASN A 570 HIS A 644 HIS A 700 HIS A 739 ASN A 805 ASN A 893 ASN A 983 HIS D 451 HIS D 460 ASN D 476 ASN D 512 HIS D 519 HIS D 549 ASN D 570 HIS D 577 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS ** D 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 HIS D 719 HIS D 805 ASN D 893 ASN D 983 HIS ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 460 ASN B 476 ASN B 512 HIS B 519 HIS B 549 ASN B 577 ASN B 590 ASN B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 983 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 476 ASN C 512 HIS C 519 HIS ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 590 ASN C 644 HIS ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN C 700 HIS C 719 HIS C 805 ASN C 893 ASN C 907 GLN C 970 HIS C 983 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094227 restraints weight = 33140.005| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.74 r_work: 0.3012 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20928 Z= 0.140 Angle : 0.716 15.821 28208 Z= 0.328 Chirality : 0.045 0.226 3224 Planarity : 0.005 0.065 3392 Dihedral : 23.127 156.553 3606 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.50 % Allowed : 11.66 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.71 (0.16), residues: 2436 helix: -0.26 (0.12), residues: 1760 sheet: 1.64 (0.79), residues: 68 loop : -0.95 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 996 TYR 0.015 0.001 TYR D 768 PHE 0.013 0.001 PHE D 823 TRP 0.014 0.002 TRP A 515 HIS 0.004 0.001 HIS A 970 Details of bonding type rmsd covalent geometry : bond 0.00301 (20916) covalent geometry : angle 0.67187 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04792 ( 1173) hydrogen bonds : angle 4.31802 ( 3471) Misc. bond : bond 0.00071 ( 4) link_BETA1-4 : bond 0.01113 ( 4) link_BETA1-4 : angle 6.18452 ( 12) link_NAG-ASN : bond 0.00446 ( 4) link_NAG-ASN : angle 10.33096 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 610 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8939 (mmtm) REVERT: A 625 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8791 (mm-30) REVERT: A 721 MET cc_start: 0.8606 (tpp) cc_final: 0.8397 (mmp) REVERT: A 783 PHE cc_start: 0.8055 (m-10) cc_final: 0.7778 (m-10) REVERT: A 852 ARG cc_start: 0.8594 (mpt180) cc_final: 0.8058 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8562 (tp30) cc_final: 0.8333 (mm-30) REVERT: D 607 GLU cc_start: 0.8356 (mp0) cc_final: 0.8058 (mp0) REVERT: D 610 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8797 (mmtp) REVERT: D 657 GLU cc_start: 0.8413 (tt0) cc_final: 0.8140 (tm-30) REVERT: D 681 GLU cc_start: 0.8367 (pm20) cc_final: 0.8139 (pm20) REVERT: D 852 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7542 (mmm-85) REVERT: D 981 GLU cc_start: 0.8795 (tp30) cc_final: 0.8199 (tp30) REVERT: D 985 SER cc_start: 0.9418 (t) cc_final: 0.8665 (p) REVERT: B 488 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 591 LYS cc_start: 0.9463 (mttt) cc_final: 0.9240 (mtmm) REVERT: B 852 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7713 (mmm-85) REVERT: B 935 VAL cc_start: 0.9453 (t) cc_final: 0.9215 (p) REVERT: B 985 SER cc_start: 0.9338 (t) cc_final: 0.9032 (p) REVERT: B 1073 GLU cc_start: 0.8078 (tt0) cc_final: 0.7517 (tt0) REVERT: B 1075 ILE cc_start: 0.8442 (mt) cc_final: 0.8147 (mp) REVERT: C 852 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: C 981 GLU cc_start: 0.8746 (tp30) cc_final: 0.8125 (tp30) REVERT: C 985 SER cc_start: 0.9304 (t) cc_final: 0.8618 (p) REVERT: C 998 VAL cc_start: 0.9116 (p) cc_final: 0.8771 (m) REVERT: C 1075 ILE cc_start: 0.8872 (mt) cc_final: 0.8473 (mp) outliers start: 52 outliers final: 17 residues processed: 395 average time/residue: 0.1243 time to fit residues: 79.7098 Evaluate side-chains 315 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 775 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 933 HIS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 175 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 179 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 ASN C 537 ASN C 687 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090126 restraints weight = 33001.121| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.70 r_work: 0.2952 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20928 Z= 0.130 Angle : 0.630 12.253 28208 Z= 0.293 Chirality : 0.042 0.219 3224 Planarity : 0.004 0.066 3392 Dihedral : 21.275 150.508 3600 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.88 % Allowed : 12.91 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.43 (0.17), residues: 2436 helix: 0.58 (0.12), residues: 1764 sheet: 4.15 (0.85), residues: 48 loop : -0.62 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 996 TYR 0.022 0.001 TYR C 768 PHE 0.014 0.001 PHE D 823 TRP 0.012 0.001 TRP A 515 HIS 0.006 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00294 (20916) covalent geometry : angle 0.60492 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04256 ( 1173) hydrogen bonds : angle 3.86823 ( 3471) Misc. bond : bond 0.00073 ( 4) link_BETA1-4 : bond 0.00516 ( 4) link_BETA1-4 : angle 3.00510 ( 12) link_NAG-ASN : bond 0.01560 ( 4) link_NAG-ASN : angle 8.11494 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 336 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 681 GLU cc_start: 0.8146 (pm20) cc_final: 0.7899 (pm20) REVERT: A 721 MET cc_start: 0.8600 (tpp) cc_final: 0.8399 (mmp) REVERT: A 783 PHE cc_start: 0.8218 (m-10) cc_final: 0.7945 (m-10) REVERT: A 852 ARG cc_start: 0.8674 (mpt180) cc_final: 0.8175 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8644 (tp30) cc_final: 0.8394 (mm-30) REVERT: D 464 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7839 (mtm110) REVERT: D 504 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8627 (mmmm) REVERT: D 643 LEU cc_start: 0.8248 (mp) cc_final: 0.7812 (mt) REVERT: D 657 GLU cc_start: 0.8540 (tt0) cc_final: 0.8194 (tm-30) REVERT: D 852 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7664 (mmm-85) REVERT: D 981 GLU cc_start: 0.8827 (tp30) cc_final: 0.8409 (tp30) REVERT: D 985 SER cc_start: 0.9373 (t) cc_final: 0.8837 (p) REVERT: D 987 GLU cc_start: 0.8767 (tt0) cc_final: 0.8536 (tt0) REVERT: B 483 MET cc_start: 0.8656 (mtt) cc_final: 0.8073 (mtp) REVERT: B 488 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8470 (mm) REVERT: B 591 LYS cc_start: 0.9439 (mttt) cc_final: 0.9217 (mtmm) REVERT: B 709 MET cc_start: 0.9283 (tmm) cc_final: 0.9014 (tmm) REVERT: B 852 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: B 912 MET cc_start: 0.9075 (ttp) cc_final: 0.8825 (ttm) REVERT: B 998 VAL cc_start: 0.9112 (p) cc_final: 0.8699 (m) REVERT: B 1059 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8515 (mm-30) REVERT: B 1075 ILE cc_start: 0.8924 (mt) cc_final: 0.8521 (mp) REVERT: C 610 LYS cc_start: 0.9121 (mmtp) cc_final: 0.8806 (mmtp) REVERT: C 852 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7821 (mmm-85) REVERT: C 981 GLU cc_start: 0.8806 (tp30) cc_final: 0.8363 (tp30) REVERT: C 985 SER cc_start: 0.9361 (t) cc_final: 0.8815 (p) REVERT: C 1075 ILE cc_start: 0.8922 (mt) cc_final: 0.8567 (mm) outliers start: 60 outliers final: 23 residues processed: 378 average time/residue: 0.1285 time to fit residues: 77.9739 Evaluate side-chains 312 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 947 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 203 optimal weight: 0.0270 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 236 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 831 GLN A 907 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1000 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090139 restraints weight = 33335.862| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.74 r_work: 0.2954 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20928 Z= 0.112 Angle : 0.596 10.954 28208 Z= 0.279 Chirality : 0.041 0.184 3224 Planarity : 0.004 0.060 3392 Dihedral : 20.032 154.911 3600 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 14.68 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.01 (0.17), residues: 2436 helix: 1.02 (0.13), residues: 1760 sheet: 4.15 (0.84), residues: 48 loop : -0.44 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 996 TYR 0.008 0.001 TYR A 842 PHE 0.009 0.001 PHE D 823 TRP 0.010 0.001 TRP A 515 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00242 (20916) covalent geometry : angle 0.57275 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03761 ( 1173) hydrogen bonds : angle 3.72455 ( 3471) Misc. bond : bond 0.00025 ( 4) link_BETA1-4 : bond 0.00740 ( 4) link_BETA1-4 : angle 3.87693 ( 12) link_NAG-ASN : bond 0.01298 ( 4) link_NAG-ASN : angle 7.06056 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.714 Fit side-chains REVERT: A 721 MET cc_start: 0.8670 (tpp) cc_final: 0.8463 (mmp) REVERT: A 783 PHE cc_start: 0.8299 (m-10) cc_final: 0.8059 (m-10) REVERT: A 785 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: A 852 ARG cc_start: 0.8678 (mpt180) cc_final: 0.8199 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8658 (tp30) cc_final: 0.8385 (mm-30) REVERT: D 464 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7845 (mtm110) REVERT: D 504 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8552 (mmmm) REVERT: D 509 LEU cc_start: 0.9277 (mm) cc_final: 0.9011 (mp) REVERT: D 657 GLU cc_start: 0.8504 (tt0) cc_final: 0.8056 (tm-30) REVERT: D 852 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: D 981 GLU cc_start: 0.8863 (tp30) cc_final: 0.8445 (tp30) REVERT: D 985 SER cc_start: 0.9383 (t) cc_final: 0.8850 (p) REVERT: D 987 GLU cc_start: 0.8757 (tt0) cc_final: 0.8515 (tt0) REVERT: B 591 LYS cc_start: 0.9447 (mttt) cc_final: 0.9233 (mtmm) REVERT: B 785 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: B 852 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7815 (mmm-85) REVERT: B 912 MET cc_start: 0.9034 (ttp) cc_final: 0.8777 (ttm) REVERT: B 946 ILE cc_start: 0.9388 (mm) cc_final: 0.9182 (mt) REVERT: B 987 GLU cc_start: 0.8808 (tt0) cc_final: 0.8461 (tt0) REVERT: B 996 ARG cc_start: 0.8991 (ttm-80) cc_final: 0.8571 (mtp85) REVERT: B 1059 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8565 (mm-30) REVERT: C 483 MET cc_start: 0.8812 (mtp) cc_final: 0.8533 (mtp) REVERT: C 610 LYS cc_start: 0.9171 (mmtp) cc_final: 0.8788 (mmtp) REVERT: C 852 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7798 (mmm-85) REVERT: C 981 GLU cc_start: 0.8789 (tp30) cc_final: 0.8394 (tp30) REVERT: C 985 SER cc_start: 0.9366 (t) cc_final: 0.8884 (p) REVERT: C 1075 ILE cc_start: 0.8915 (mt) cc_final: 0.8510 (mm) outliers start: 49 outliers final: 26 residues processed: 342 average time/residue: 0.1294 time to fit residues: 71.8720 Evaluate side-chains 305 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain D residue 1069 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 181 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 242 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN D 481 HIS D 560 HIS B 692 ASN B 907 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086714 restraints weight = 33099.478| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.69 r_work: 0.2893 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20928 Z= 0.132 Angle : 0.588 9.908 28208 Z= 0.277 Chirality : 0.041 0.176 3224 Planarity : 0.004 0.060 3392 Dihedral : 18.958 160.806 3600 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.30 % Allowed : 14.97 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.35 (0.18), residues: 2436 helix: 1.28 (0.13), residues: 1760 sheet: 4.38 (0.82), residues: 48 loop : -0.32 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 996 TYR 0.024 0.001 TYR C 768 PHE 0.010 0.001 PHE C 994 TRP 0.011 0.001 TRP A 515 HIS 0.006 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00310 (20916) covalent geometry : angle 0.56850 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03937 ( 1173) hydrogen bonds : angle 3.67300 ( 3471) Misc. bond : bond 0.00043 ( 4) link_BETA1-4 : bond 0.00796 ( 4) link_BETA1-4 : angle 3.57764 ( 12) link_NAG-ASN : bond 0.01126 ( 4) link_NAG-ASN : angle 6.36679 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 0.756 Fit side-chains REVERT: A 464 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7569 (tmm160) REVERT: A 720 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: A 721 MET cc_start: 0.8702 (tpp) cc_final: 0.8478 (mmp) REVERT: A 783 PHE cc_start: 0.8396 (m-10) cc_final: 0.8108 (m-10) REVERT: A 785 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: A 852 ARG cc_start: 0.8693 (mpt180) cc_final: 0.8184 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8698 (tp30) cc_final: 0.8389 (mm-30) REVERT: D 464 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7859 (mtm110) REVERT: D 503 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8795 (ttpt) REVERT: D 852 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7754 (mmm-85) REVERT: D 981 GLU cc_start: 0.8851 (tp30) cc_final: 0.8418 (tp30) REVERT: D 985 SER cc_start: 0.9425 (t) cc_final: 0.8902 (p) REVERT: D 987 GLU cc_start: 0.8771 (tt0) cc_final: 0.8500 (tt0) REVERT: B 591 LYS cc_start: 0.9447 (mttt) cc_final: 0.9229 (mtmm) REVERT: B 781 SER cc_start: 0.8821 (m) cc_final: 0.8595 (p) REVERT: B 785 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: B 852 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7818 (mmm-85) REVERT: B 912 MET cc_start: 0.9122 (ttp) cc_final: 0.8873 (ttm) REVERT: B 941 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 987 GLU cc_start: 0.8819 (tt0) cc_final: 0.8417 (tt0) REVERT: B 1059 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8568 (mm-30) REVERT: C 483 MET cc_start: 0.8943 (mtp) cc_final: 0.8672 (mtp) REVERT: C 610 LYS cc_start: 0.9247 (mmtp) cc_final: 0.8850 (mmtp) REVERT: C 852 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: C 941 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8976 (tp) REVERT: C 981 GLU cc_start: 0.8821 (tp30) cc_final: 0.8287 (tp30) REVERT: C 985 SER cc_start: 0.9406 (t) cc_final: 0.8746 (p) outliers start: 48 outliers final: 30 residues processed: 317 average time/residue: 0.1256 time to fit residues: 64.0438 Evaluate side-chains 296 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 186 optimal weight: 0.0980 chunk 214 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS C 619 ASN C 739 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087528 restraints weight = 33027.294| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.73 r_work: 0.2915 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20928 Z= 0.107 Angle : 0.564 9.875 28208 Z= 0.264 Chirality : 0.040 0.172 3224 Planarity : 0.004 0.057 3392 Dihedral : 18.212 165.795 3600 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.35 % Allowed : 16.07 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.58 (0.18), residues: 2436 helix: 1.45 (0.13), residues: 1756 sheet: 4.28 (0.82), residues: 48 loop : -0.21 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 996 TYR 0.013 0.001 TYR C 842 PHE 0.007 0.001 PHE C 583 TRP 0.009 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00238 (20916) covalent geometry : angle 0.54758 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03577 ( 1173) hydrogen bonds : angle 3.60625 ( 3471) Misc. bond : bond 0.00031 ( 4) link_BETA1-4 : bond 0.00771 ( 4) link_BETA1-4 : angle 3.55084 ( 12) link_NAG-ASN : bond 0.01055 ( 4) link_NAG-ASN : angle 5.48055 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.827 Fit side-chains REVERT: A 464 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7576 (tmm160) REVERT: A 530 MET cc_start: 0.8883 (mtm) cc_final: 0.8653 (mtm) REVERT: A 721 MET cc_start: 0.8653 (tpp) cc_final: 0.8434 (mmp) REVERT: A 783 PHE cc_start: 0.8398 (m-10) cc_final: 0.8092 (m-10) REVERT: A 785 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7843 (m-10) REVERT: A 852 ARG cc_start: 0.8672 (mpt180) cc_final: 0.8206 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8723 (tp30) cc_final: 0.8474 (mm-30) REVERT: D 464 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7862 (mtm110) REVERT: D 852 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: D 981 GLU cc_start: 0.8826 (tp30) cc_final: 0.8456 (tp30) REVERT: D 985 SER cc_start: 0.9418 (t) cc_final: 0.8972 (p) REVERT: D 987 GLU cc_start: 0.8761 (tt0) cc_final: 0.8536 (tt0) REVERT: B 591 LYS cc_start: 0.9457 (mttt) cc_final: 0.9237 (mtmm) REVERT: B 781 SER cc_start: 0.8808 (m) cc_final: 0.8599 (p) REVERT: B 785 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: B 852 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7808 (mmm-85) REVERT: B 912 MET cc_start: 0.9105 (ttp) cc_final: 0.8854 (ttm) REVERT: B 941 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 981 GLU cc_start: 0.8596 (tp30) cc_final: 0.8382 (tm-30) REVERT: B 987 GLU cc_start: 0.8839 (tt0) cc_final: 0.8457 (tt0) REVERT: C 483 MET cc_start: 0.8922 (mtp) cc_final: 0.8645 (mtp) REVERT: C 610 LYS cc_start: 0.9247 (mmtp) cc_final: 0.8823 (mmtp) REVERT: C 852 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7796 (mmm-85) REVERT: C 912 MET cc_start: 0.9060 (ttp) cc_final: 0.8759 (ttm) REVERT: C 941 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9040 (tp) REVERT: C 981 GLU cc_start: 0.8775 (tp30) cc_final: 0.8393 (tp30) REVERT: C 985 SER cc_start: 0.9394 (t) cc_final: 0.8922 (p) outliers start: 49 outliers final: 30 residues processed: 306 average time/residue: 0.1349 time to fit residues: 67.2330 Evaluate side-chains 287 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain D residue 1069 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 494 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.120621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086744 restraints weight = 33040.999| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.73 r_work: 0.2902 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20928 Z= 0.110 Angle : 0.564 8.962 28208 Z= 0.264 Chirality : 0.040 0.157 3224 Planarity : 0.004 0.057 3392 Dihedral : 17.699 171.709 3600 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 15.74 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.73 (0.18), residues: 2436 helix: 1.53 (0.13), residues: 1760 sheet: 4.30 (0.80), residues: 48 loop : -0.09 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 996 TYR 0.016 0.001 TYR D 842 PHE 0.018 0.001 PHE B1022 TRP 0.009 0.001 TRP D 809 HIS 0.005 0.001 HIS D 481 Details of bonding type rmsd covalent geometry : bond 0.00251 (20916) covalent geometry : angle 0.55057 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03580 ( 1173) hydrogen bonds : angle 3.56492 ( 3471) Misc. bond : bond 0.00043 ( 4) link_BETA1-4 : bond 0.00785 ( 4) link_BETA1-4 : angle 3.36388 ( 12) link_NAG-ASN : bond 0.00912 ( 4) link_NAG-ASN : angle 4.96756 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.726 Fit side-chains REVERT: A 464 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7567 (tmm160) REVERT: A 530 MET cc_start: 0.8920 (mtm) cc_final: 0.8679 (mtm) REVERT: A 720 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 721 MET cc_start: 0.8671 (tpp) cc_final: 0.8429 (mmp) REVERT: A 783 PHE cc_start: 0.8406 (m-10) cc_final: 0.8094 (m-10) REVERT: A 785 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7909 (m-10) REVERT: A 852 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8272 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8789 (tp30) cc_final: 0.8484 (mm-30) REVERT: D 464 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7792 (mtm110) REVERT: D 809 TRP cc_start: 0.8942 (m100) cc_final: 0.8698 (m100) REVERT: D 852 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7792 (mmm-85) REVERT: D 981 GLU cc_start: 0.8843 (tp30) cc_final: 0.8453 (tp30) REVERT: D 985 SER cc_start: 0.9427 (t) cc_final: 0.8956 (p) REVERT: D 987 GLU cc_start: 0.8778 (tt0) cc_final: 0.8519 (tt0) REVERT: B 591 LYS cc_start: 0.9441 (mttt) cc_final: 0.9217 (mtmm) REVERT: B 785 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7844 (m-10) REVERT: B 852 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7776 (mmm-85) REVERT: B 912 MET cc_start: 0.9128 (ttp) cc_final: 0.8858 (ttm) REVERT: B 941 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 985 SER cc_start: 0.9391 (t) cc_final: 0.9013 (p) REVERT: B 987 GLU cc_start: 0.8743 (tt0) cc_final: 0.8330 (tt0) REVERT: C 610 LYS cc_start: 0.9275 (mmtp) cc_final: 0.8854 (mmtp) REVERT: C 852 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7780 (mmm-85) REVERT: C 912 MET cc_start: 0.9135 (ttp) cc_final: 0.8764 (ttm) REVERT: C 981 GLU cc_start: 0.8801 (tp30) cc_final: 0.8275 (tp30) REVERT: C 985 SER cc_start: 0.9411 (t) cc_final: 0.8762 (p) outliers start: 49 outliers final: 30 residues processed: 303 average time/residue: 0.1354 time to fit residues: 66.2620 Evaluate side-chains 297 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 15 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 161 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 211 optimal weight: 0.3980 chunk 225 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087180 restraints weight = 33109.027| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.74 r_work: 0.2910 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20928 Z= 0.103 Angle : 0.555 11.542 28208 Z= 0.259 Chirality : 0.039 0.164 3224 Planarity : 0.003 0.057 3392 Dihedral : 17.191 179.333 3600 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.02 % Allowed : 16.12 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.80 (0.18), residues: 2436 helix: 1.59 (0.13), residues: 1760 sheet: 4.25 (0.79), residues: 48 loop : -0.05 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 464 TYR 0.013 0.001 TYR A 768 PHE 0.022 0.001 PHE C1022 TRP 0.010 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00229 (20916) covalent geometry : angle 0.54421 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03423 ( 1173) hydrogen bonds : angle 3.53605 ( 3471) Misc. bond : bond 0.00034 ( 4) link_BETA1-4 : bond 0.00756 ( 4) link_BETA1-4 : angle 3.04009 ( 12) link_NAG-ASN : bond 0.00838 ( 4) link_NAG-ASN : angle 4.48987 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.819 Fit side-chains REVERT: A 464 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7650 (tmm160) REVERT: A 530 MET cc_start: 0.8953 (mtm) cc_final: 0.8735 (mtm) REVERT: A 721 MET cc_start: 0.8653 (tpp) cc_final: 0.8450 (mmp) REVERT: A 783 PHE cc_start: 0.8302 (m-10) cc_final: 0.8012 (m-10) REVERT: A 785 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: A 852 ARG cc_start: 0.8714 (mpt180) cc_final: 0.8228 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8799 (tp30) cc_final: 0.8497 (mm-30) REVERT: D 464 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7826 (mtm110) REVERT: D 625 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8927 (mm-30) REVERT: D 809 TRP cc_start: 0.8941 (m100) cc_final: 0.8672 (m100) REVERT: D 852 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7797 (mmm-85) REVERT: D 941 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9021 (tp) REVERT: D 981 GLU cc_start: 0.8834 (tp30) cc_final: 0.8442 (tp30) REVERT: D 985 SER cc_start: 0.9422 (t) cc_final: 0.8937 (p) REVERT: D 987 GLU cc_start: 0.8785 (tt0) cc_final: 0.8526 (tt0) REVERT: B 591 LYS cc_start: 0.9446 (mttt) cc_final: 0.9220 (mtmm) REVERT: B 785 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: B 852 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: B 912 MET cc_start: 0.9133 (ttp) cc_final: 0.8866 (ttm) REVERT: B 981 GLU cc_start: 0.8637 (tp30) cc_final: 0.8331 (tm-30) REVERT: B 985 SER cc_start: 0.9381 (t) cc_final: 0.9127 (p) REVERT: B 987 GLU cc_start: 0.8769 (tt0) cc_final: 0.8325 (tt0) REVERT: B 1059 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8539 (mm-30) REVERT: C 464 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7571 (ttp80) REVERT: C 610 LYS cc_start: 0.9292 (mmtp) cc_final: 0.8879 (mmtp) REVERT: C 852 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: C 912 MET cc_start: 0.9174 (ttp) cc_final: 0.8759 (ttm) REVERT: C 981 GLU cc_start: 0.8784 (tp30) cc_final: 0.8267 (tp30) REVERT: C 985 SER cc_start: 0.9413 (t) cc_final: 0.8756 (p) outliers start: 42 outliers final: 30 residues processed: 302 average time/residue: 0.1418 time to fit residues: 69.3320 Evaluate side-chains 296 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain D residue 1069 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 39 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 73 optimal weight: 0.0070 chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 481 HIS D 692 ASN ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.086830 restraints weight = 32919.690| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.73 r_work: 0.2906 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20928 Z= 0.103 Angle : 0.549 9.746 28208 Z= 0.256 Chirality : 0.039 0.156 3224 Planarity : 0.003 0.056 3392 Dihedral : 16.812 179.528 3600 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.92 % Allowed : 16.03 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.88 (0.18), residues: 2436 helix: 1.65 (0.13), residues: 1760 sheet: 4.15 (0.79), residues: 48 loop : -0.03 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.017 0.001 TYR B 768 PHE 0.020 0.001 PHE B1022 TRP 0.010 0.001 TRP D 809 HIS 0.006 0.001 HIS D 481 Details of bonding type rmsd covalent geometry : bond 0.00233 (20916) covalent geometry : angle 0.53966 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03431 ( 1173) hydrogen bonds : angle 3.49778 ( 3471) Misc. bond : bond 0.00036 ( 4) link_BETA1-4 : bond 0.00742 ( 4) link_BETA1-4 : angle 2.74956 ( 12) link_NAG-ASN : bond 0.00740 ( 4) link_NAG-ASN : angle 4.26883 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.775 Fit side-chains REVERT: A 464 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7595 (ttp80) REVERT: A 530 MET cc_start: 0.8960 (mtm) cc_final: 0.8746 (mtm) REVERT: A 720 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8286 (mmm) REVERT: A 721 MET cc_start: 0.8657 (tpp) cc_final: 0.8443 (mmp) REVERT: A 783 PHE cc_start: 0.8252 (m-10) cc_final: 0.7989 (m-10) REVERT: A 785 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: A 852 ARG cc_start: 0.8690 (mpt180) cc_final: 0.8211 (mmm-85) REVERT: A 981 GLU cc_start: 0.8698 (tp30) cc_final: 0.8494 (tm-30) REVERT: A 1059 GLU cc_start: 0.8822 (tp30) cc_final: 0.8515 (mm-30) REVERT: D 464 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7826 (mtm110) REVERT: D 625 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8909 (mm-30) REVERT: D 634 MET cc_start: 0.9195 (tpt) cc_final: 0.8935 (tpt) REVERT: D 809 TRP cc_start: 0.8937 (m100) cc_final: 0.8671 (m100) REVERT: D 852 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7811 (mmm-85) REVERT: D 941 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9008 (tp) REVERT: D 981 GLU cc_start: 0.8835 (tp30) cc_final: 0.8369 (tp30) REVERT: D 985 SER cc_start: 0.9429 (t) cc_final: 0.8805 (p) REVERT: D 987 GLU cc_start: 0.8779 (tt0) cc_final: 0.8476 (tt0) REVERT: B 591 LYS cc_start: 0.9451 (mttt) cc_final: 0.9223 (mtmm) REVERT: B 785 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: B 852 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: B 912 MET cc_start: 0.9150 (ttp) cc_final: 0.8872 (ttm) REVERT: B 981 GLU cc_start: 0.8626 (tp30) cc_final: 0.8321 (tm-30) REVERT: B 985 SER cc_start: 0.9369 (t) cc_final: 0.9107 (p) REVERT: B 987 GLU cc_start: 0.8753 (tt0) cc_final: 0.8318 (tt0) REVERT: B 1059 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8545 (mm-30) REVERT: C 464 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7587 (ttp80) REVERT: C 610 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8855 (mmtp) REVERT: C 634 MET cc_start: 0.9109 (tpt) cc_final: 0.8860 (tpt) REVERT: C 852 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: C 912 MET cc_start: 0.9195 (ttp) cc_final: 0.8782 (ttm) REVERT: C 981 GLU cc_start: 0.8799 (tp30) cc_final: 0.8280 (tp30) REVERT: C 985 SER cc_start: 0.9430 (t) cc_final: 0.8741 (p) outliers start: 40 outliers final: 30 residues processed: 298 average time/residue: 0.1423 time to fit residues: 68.7007 Evaluate side-chains 298 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 151 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 185 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086562 restraints weight = 33108.050| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.75 r_work: 0.2895 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20928 Z= 0.107 Angle : 0.548 9.790 28208 Z= 0.258 Chirality : 0.039 0.161 3224 Planarity : 0.003 0.056 3392 Dihedral : 16.375 176.212 3600 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.92 % Allowed : 16.03 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.94 (0.18), residues: 2436 helix: 1.70 (0.13), residues: 1760 sheet: 4.10 (0.78), residues: 48 loop : -0.01 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.012 0.001 TYR D 840 PHE 0.024 0.001 PHE C1022 TRP 0.012 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00245 (20916) covalent geometry : angle 0.53907 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03481 ( 1173) hydrogen bonds : angle 3.51029 ( 3471) Misc. bond : bond 0.00040 ( 4) link_BETA1-4 : bond 0.00750 ( 4) link_BETA1-4 : angle 2.37633 ( 12) link_NAG-ASN : bond 0.00692 ( 4) link_NAG-ASN : angle 4.14238 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.791 Fit side-chains REVERT: A 464 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7620 (ttp80) REVERT: A 530 MET cc_start: 0.8965 (mtm) cc_final: 0.8751 (mtm) REVERT: A 681 GLU cc_start: 0.8393 (pm20) cc_final: 0.8169 (pm20) REVERT: A 721 MET cc_start: 0.8648 (tpp) cc_final: 0.8438 (mmp) REVERT: A 783 PHE cc_start: 0.8261 (m-10) cc_final: 0.7990 (m-10) REVERT: A 785 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: A 852 ARG cc_start: 0.8694 (mpt180) cc_final: 0.8216 (mmm-85) REVERT: A 981 GLU cc_start: 0.8711 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 1059 GLU cc_start: 0.8833 (tp30) cc_final: 0.8526 (mm-30) REVERT: D 625 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8913 (mm-30) REVERT: D 852 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7779 (mmm-85) REVERT: D 941 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9026 (tp) REVERT: D 981 GLU cc_start: 0.8853 (tp30) cc_final: 0.8389 (tp30) REVERT: D 985 SER cc_start: 0.9429 (t) cc_final: 0.8819 (p) REVERT: D 987 GLU cc_start: 0.8787 (tt0) cc_final: 0.8537 (tt0) REVERT: B 591 LYS cc_start: 0.9461 (mttt) cc_final: 0.9240 (mtmm) REVERT: B 785 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: B 852 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: B 912 MET cc_start: 0.9165 (ttp) cc_final: 0.8893 (ttm) REVERT: B 981 GLU cc_start: 0.8664 (tp30) cc_final: 0.8341 (tm-30) REVERT: B 985 SER cc_start: 0.9370 (t) cc_final: 0.9082 (p) REVERT: B 987 GLU cc_start: 0.8804 (tt0) cc_final: 0.8381 (tt0) REVERT: B 1059 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8596 (mm-30) REVERT: C 464 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7574 (ttp80) REVERT: C 852 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: C 912 MET cc_start: 0.9198 (ttp) cc_final: 0.8793 (ttm) REVERT: C 981 GLU cc_start: 0.8787 (tp30) cc_final: 0.8276 (tp30) REVERT: C 985 SER cc_start: 0.9441 (t) cc_final: 0.8786 (p) outliers start: 40 outliers final: 28 residues processed: 293 average time/residue: 0.1417 time to fit residues: 67.4013 Evaluate side-chains 289 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 886 LEU Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 174 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 110 optimal weight: 0.0030 chunk 199 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.086097 restraints weight = 33131.366| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.74 r_work: 0.2895 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20928 Z= 0.106 Angle : 0.546 9.453 28208 Z= 0.257 Chirality : 0.039 0.159 3224 Planarity : 0.003 0.056 3392 Dihedral : 15.987 173.673 3600 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.68 % Allowed : 16.27 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.97 (0.18), residues: 2436 helix: 1.77 (0.13), residues: 1736 sheet: 4.06 (0.78), residues: 48 loop : -0.08 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.011 0.001 TYR D 842 PHE 0.018 0.001 PHE A1022 TRP 0.011 0.001 TRP D 809 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00243 (20916) covalent geometry : angle 0.53910 (28168) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.03453 ( 1173) hydrogen bonds : angle 3.46958 ( 3471) Misc. bond : bond 0.00037 ( 4) link_BETA1-4 : bond 0.00665 ( 4) link_BETA1-4 : angle 2.08450 ( 12) link_NAG-ASN : bond 0.00643 ( 4) link_NAG-ASN : angle 3.80613 ( 12) =============================================================================== Job complete usr+sys time: 4480.75 seconds wall clock time: 77 minutes 38.68 seconds (4658.68 seconds total)