Starting phenix.real_space_refine on Wed Mar 4 07:57:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lzi_23607/03_2026/7lzi_23607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lzi_23607/03_2026/7lzi_23607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lzi_23607/03_2026/7lzi_23607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lzi_23607/03_2026/7lzi_23607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lzi_23607/03_2026/7lzi_23607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lzi_23607/03_2026/7lzi_23607.map" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7638 2.51 5 N 1934 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11782 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2946 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2869 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2946 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2869 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11782 At special positions: 0 Unit cell: (107.07, 110.39, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2172 8.00 N 1934 7.00 C 7638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 841 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 841 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 576 " " NAG F 1 " - " ASN B 576 " " NAG G 1 " - " ASN C 576 " " NAG H 1 " - " ASN D 576 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 590.9 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 16 sheets defined 50.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.691A pdb=" N ILE A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.678A pdb=" N ARG A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 613 through 635 removed outlier: 3.782A pdb=" N ALA A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 621 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 630 " --> pdb=" O PHE A 626 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 659 removed outlier: 3.893A pdb=" N SER A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 703 removed outlier: 3.620A pdb=" N ILE A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 728 through 737 removed outlier: 4.454A pdb=" N ASN A 732 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 736 " --> pdb=" O ASN A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.623A pdb=" N LEU A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.694A pdb=" N VAL A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 825 removed outlier: 3.972A pdb=" N ASP A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 861 through 880 removed outlier: 3.504A pdb=" N VAL A 875 " --> pdb=" O MET A 871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 530 removed outlier: 3.637A pdb=" N ALA B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 removed outlier: 3.810A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.811A pdb=" N TYR B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.881A pdb=" N PHE B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.953A pdb=" N ALA B 618 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B 630 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 631 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.560A pdb=" N PHE B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 701 removed outlier: 3.540A pdb=" N ILE B 679 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 687 " --> pdb=" O PHE B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 712 through 717 Processing helix chain 'B' and resid 728 through 737 removed outlier: 4.573A pdb=" N ASN B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 735 " --> pdb=" O ARG B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.749A pdb=" N LEU B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 758 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 784 removed outlier: 3.799A pdb=" N VAL B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 825 removed outlier: 3.846A pdb=" N ASP B 813 " --> pdb=" O PRO B 809 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 814 " --> pdb=" O LEU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 835 Processing helix chain 'B' and resid 859 through 880 removed outlier: 3.626A pdb=" N ILE B 864 " --> pdb=" O GLY B 860 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS B 869 " --> pdb=" O CYS B 865 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 874 " --> pdb=" O PHE B 870 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 532 removed outlier: 3.690A pdb=" N ILE C 529 " --> pdb=" O PHE C 525 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 561 Processing helix chain 'C' and resid 574 through 581 removed outlier: 3.678A pdb=" N ARG C 579 " --> pdb=" O THR C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 613 through 635 removed outlier: 3.782A pdb=" N ALA C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 621 " --> pdb=" O TRP C 617 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 625 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 659 removed outlier: 3.893A pdb=" N SER C 657 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 703 removed outlier: 3.621A pdb=" N ILE C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 699 " --> pdb=" O SER C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'C' and resid 728 through 737 removed outlier: 4.455A pdb=" N ASN C 732 " --> pdb=" O THR C 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 736 " --> pdb=" O ASN C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 760 removed outlier: 3.623A pdb=" N LEU C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 756 " --> pdb=" O GLU C 752 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 758 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 784 removed outlier: 3.693A pdb=" N VAL C 779 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 825 removed outlier: 3.972A pdb=" N ASP C 813 " --> pdb=" O PRO C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 861 through 880 removed outlier: 3.504A pdb=" N VAL C 875 " --> pdb=" O MET C 871 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 530 removed outlier: 3.637A pdb=" N ALA D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 561 removed outlier: 3.810A pdb=" N VAL D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.811A pdb=" N TYR D 580 " --> pdb=" O ASN D 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 581 " --> pdb=" O ARG D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 removed outlier: 3.881A pdb=" N PHE D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 609 " --> pdb=" O PRO D 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 604 through 609' Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.953A pdb=" N ALA D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET D 630 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 631 " --> pdb=" O VAL D 627 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 633 " --> pdb=" O ALA D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.560A pdb=" N PHE D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 659 " --> pdb=" O TRP D 655 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 701 removed outlier: 3.540A pdb=" N ILE D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 687 " --> pdb=" O PHE D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 728 through 737 removed outlier: 4.573A pdb=" N ASN D 732 " --> pdb=" O THR D 728 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 735 " --> pdb=" O ARG D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 760 removed outlier: 3.749A pdb=" N LEU D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 758 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 784 removed outlier: 3.798A pdb=" N VAL D 779 " --> pdb=" O PRO D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 825 removed outlier: 3.846A pdb=" N ASP D 813 " --> pdb=" O PRO D 809 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 814 " --> pdb=" O LEU D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 835 Processing helix chain 'D' and resid 859 through 880 removed outlier: 3.627A pdb=" N ILE D 864 " --> pdb=" O GLY D 860 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS D 869 " --> pdb=" O CYS D 865 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 870 " --> pdb=" O GLY D 866 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 874 " --> pdb=" O PHE D 870 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 875 " --> pdb=" O MET D 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 539 through 542 removed outlier: 3.510A pdb=" N ILE A 496 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510 Processing sheet with id=AA3, first strand: chain 'A' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE A 722 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 748 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 724 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN A 725 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU A 773 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 596 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE A 722 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 748 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 724 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN A 725 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU A 773 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 796 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.732A pdb=" N ILE B 496 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA7, first strand: chain 'B' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE B 722 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 748 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 724 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 723 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLU B 773 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLN B 725 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE B 722 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 748 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 724 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 723 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLU B 773 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLN B 725 " --> pdb=" O GLU B 773 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR B 796 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 539 through 542 removed outlier: 3.510A pdb=" N ILE C 496 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 508 through 510 Processing sheet with id=AB2, first strand: chain 'C' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE C 722 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 748 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 724 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN C 725 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU C 773 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 596 " --> pdb=" O ARG C 789 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE C 722 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 748 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 724 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN C 725 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU C 773 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR C 796 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.732A pdb=" N ILE D 496 " --> pdb=" O THR D 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AB6, first strand: chain 'D' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE D 722 " --> pdb=" O VAL D 746 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU D 748 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 724 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY D 723 " --> pdb=" O VAL D 771 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU D 773 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N GLN D 725 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE D 722 " --> pdb=" O VAL D 746 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU D 748 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 724 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY D 723 " --> pdb=" O VAL D 771 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU D 773 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N GLN D 725 " --> pdb=" O GLU D 773 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR D 796 " --> pdb=" O LEU D 592 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3706 1.34 - 1.46: 2886 1.46 - 1.58: 5412 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 12060 Sorted by residual: bond pdb=" C LEU B 774 " pdb=" N PRO B 775 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.06e-02 8.90e+03 1.40e+01 bond pdb=" C LEU D 774 " pdb=" N PRO D 775 " ideal model delta sigma weight residual 1.337 1.376 -0.039 1.06e-02 8.90e+03 1.38e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" N ASN D 719 " pdb=" CA ASN D 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.06e+00 ... (remaining 12055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 16125 2.76 - 5.51: 250 5.51 - 8.27: 43 8.27 - 11.02: 4 11.02 - 13.78: 2 Bond angle restraints: 16424 Sorted by residual: angle pdb=" C SER C 718 " pdb=" N ASN C 719 " pdb=" CA ASN C 719 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C SER A 718 " pdb=" N ASN A 719 " pdb=" CA ASN A 719 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C SER D 603 " pdb=" N SER D 604 " pdb=" CA SER D 604 " ideal model delta sigma weight residual 122.29 128.43 -6.14 1.48e+00 4.57e-01 1.72e+01 angle pdb=" C SER B 603 " pdb=" N SER B 604 " pdb=" CA SER B 604 " ideal model delta sigma weight residual 122.29 128.39 -6.10 1.48e+00 4.57e-01 1.70e+01 angle pdb=" CA LEU B 609 " pdb=" CB LEU B 609 " pdb=" CG LEU B 609 " ideal model delta sigma weight residual 116.30 130.08 -13.78 3.50e+00 8.16e-02 1.55e+01 ... (remaining 16419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 6857 20.55 - 41.10: 271 41.10 - 61.65: 40 61.65 - 82.20: 12 82.20 - 102.75: 16 Dihedral angle restraints: 7196 sinusoidal: 2910 harmonic: 4286 Sorted by residual: dihedral pdb=" CA PHE A 623 " pdb=" C PHE A 623 " pdb=" N PHE A 624 " pdb=" CA PHE A 624 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE C 623 " pdb=" C PHE C 623 " pdb=" N PHE C 624 " pdb=" CA PHE C 624 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA THR B 613 " pdb=" C THR B 613 " pdb=" N ILE B 614 " pdb=" CA ILE B 614 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 1892 0.205 - 0.411: 4 0.411 - 0.616: 0 0.616 - 0.821: 1 0.821 - 1.027: 1 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 576 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 576 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" CA ASN A 719 " pdb=" N ASN A 719 " pdb=" C ASN A 719 " pdb=" CB ASN A 719 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1895 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 576 " 0.005 2.00e-02 2.50e+03 3.35e-02 1.40e+01 pdb=" CG ASN A 576 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 576 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 576 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 612 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C PHE B 612 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE B 612 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 613 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 612 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C PHE D 612 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE D 612 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 613 " 0.018 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2263 2.77 - 3.30: 11140 3.30 - 3.83: 19136 3.83 - 4.37: 22411 4.37 - 4.90: 36977 Nonbonded interactions: 91927 Sorted by model distance: nonbonded pdb=" OG1 THR A 613 " pdb=" O LYS D 856 " model vdw 2.234 3.040 nonbonded pdb=" O TRP B 485 " pdb=" OH TYR B 534 " model vdw 2.272 3.040 nonbonded pdb=" O TRP D 485 " pdb=" OH TYR D 534 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU B 526 " pdb=" OH TYR B 540 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU D 526 " pdb=" OH TYR D 540 " model vdw 2.300 3.040 ... (remaining 91922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 483 through 842 or resid 853 through 1001)) selection = chain 'B' selection = (chain 'C' and (resid 483 through 842 or resid 853 through 1001)) selection = chain 'D' } 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 group one per residue 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12072 Z= 0.248 Angle : 0.976 15.363 16456 Z= 0.533 Chirality : 0.063 1.027 1898 Planarity : 0.007 0.060 2072 Dihedral : 13.062 102.751 4416 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.32 % Allowed : 6.35 % Favored : 93.33 % 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 are not related in a simple way. whole: -4.68 (0.16), residues: 1452 helix: -3.50 (0.12), residues: 700 sheet: -2.84 (0.33), residues: 180 loop : -2.35 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 548 TYR 0.024 0.002 TYR C 552 PHE 0.018 0.002 PHE B 795 TRP 0.017 0.002 TRP A 681 HIS 0.004 0.001 HIS D 831 Details of bonding type rmsd covalent geometry : bond 0.00484 (12060) covalent geometry : angle 0.94027 (16424) SS BOND : bond 0.00122 ( 4) SS BOND : angle 2.12299 ( 8) hydrogen bonds : bond 0.29658 ( 482) hydrogen bonds : angle 9.39239 ( 1464) link_BETA1-4 : bond 0.02179 ( 4) link_BETA1-4 : angle 4.47426 ( 12) link_NAG-ASN : bond 0.03804 ( 4) link_NAG-ASN : angle 8.57110 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 516 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 VAL cc_start: 0.9305 (t) cc_final: 0.8994 (t) REVERT: A 570 ASP cc_start: 0.7785 (m-30) cc_final: 0.7170 (m-30) REVERT: A 585 GLN cc_start: 0.9079 (mm110) cc_final: 0.8725 (mm-40) REVERT: A 626 PHE cc_start: 0.7548 (t80) cc_final: 0.7138 (t80) REVERT: A 678 LEU cc_start: 0.8576 (tp) cc_final: 0.8326 (tt) REVERT: A 679 ILE cc_start: 0.8577 (mt) cc_final: 0.8321 (tp) REVERT: A 688 ILE cc_start: 0.9462 (mm) cc_final: 0.9135 (tp) REVERT: A 695 SER cc_start: 0.9191 (m) cc_final: 0.8743 (p) REVERT: A 700 LEU cc_start: 0.9435 (mm) cc_final: 0.9225 (mt) REVERT: A 749 LYS cc_start: 0.7519 (ptmt) cc_final: 0.7155 (ptpp) REVERT: A 750 ASP cc_start: 0.7067 (p0) cc_final: 0.6305 (t70) REVERT: A 790 THR cc_start: 0.8367 (p) cc_final: 0.8122 (p) REVERT: A 814 MET cc_start: 0.9281 (mtp) cc_final: 0.9069 (mtp) REVERT: B 496 ILE cc_start: 0.8632 (mp) cc_final: 0.8259 (mt) REVERT: B 554 ASN cc_start: 0.9125 (m-40) cc_final: 0.8714 (t0) REVERT: B 558 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 564 PHE cc_start: 0.8346 (m-80) cc_final: 0.8049 (m-10) REVERT: B 599 LYS cc_start: 0.6125 (pmmt) cc_final: 0.5677 (mtpt) REVERT: B 610 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8346 (tptt) REVERT: B 611 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8273 (Cg_endo) REVERT: B 626 PHE cc_start: 0.8081 (t80) cc_final: 0.7807 (t80) REVERT: B 689 ASN cc_start: 0.8589 (t0) cc_final: 0.8354 (t0) REVERT: B 692 TYR cc_start: 0.8841 (t80) cc_final: 0.8459 (t80) REVERT: B 700 LEU cc_start: 0.9234 (mm) cc_final: 0.8928 (mm) REVERT: B 703 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8269 (mtp85) REVERT: B 746 VAL cc_start: 0.9076 (t) cc_final: 0.8807 (m) REVERT: B 754 TYR cc_start: 0.9155 (m-10) cc_final: 0.8800 (m-80) REVERT: B 767 VAL cc_start: 0.8560 (m) cc_final: 0.8348 (m) REVERT: B 793 GLN cc_start: 0.8334 (mt0) cc_final: 0.8008 (mm110) REVERT: B 818 ILE cc_start: 0.9218 (mt) cc_final: 0.8934 (tp) REVERT: C 513 ASN cc_start: 0.8041 (m-40) cc_final: 0.7106 (p0) REVERT: C 521 CYS cc_start: 0.8709 (m) cc_final: 0.8217 (m) REVERT: C 547 LYS cc_start: 0.8464 (pptt) cc_final: 0.7460 (tppt) REVERT: C 552 TYR cc_start: 0.7501 (m-10) cc_final: 0.6743 (m-10) REVERT: C 554 ASN cc_start: 0.9015 (m-40) cc_final: 0.8777 (m-40) REVERT: C 602 LYS cc_start: 0.7222 (mppt) cc_final: 0.6923 (tppt) REVERT: C 681 TRP cc_start: 0.8094 (t60) cc_final: 0.7851 (t60) REVERT: C 688 ILE cc_start: 0.9168 (mm) cc_final: 0.8858 (tp) REVERT: C 700 LEU cc_start: 0.9056 (mm) cc_final: 0.8854 (mt) REVERT: C 750 ASP cc_start: 0.7135 (p0) cc_final: 0.6077 (t70) REVERT: C 751 GLU cc_start: 0.7761 (pt0) cc_final: 0.7382 (pm20) REVERT: C 754 TYR cc_start: 0.7921 (m-10) cc_final: 0.7368 (m-80) REVERT: C 779 VAL cc_start: 0.9261 (t) cc_final: 0.8889 (t) REVERT: C 794 GLU cc_start: 0.7618 (mp0) cc_final: 0.7221 (mt-10) REVERT: C 826 GLU cc_start: 0.8331 (tp30) cc_final: 0.8127 (tp30) REVERT: D 532 LEU cc_start: 0.8026 (mt) cc_final: 0.7793 (tp) REVERT: D 554 ASN cc_start: 0.9287 (m-40) cc_final: 0.9081 (t0) REVERT: D 572 THR cc_start: 0.9022 (m) cc_final: 0.8430 (p) REVERT: D 599 LYS cc_start: 0.6178 (pmmt) cc_final: 0.5863 (mtpt) REVERT: D 610 LYS cc_start: 0.8456 (ttpt) cc_final: 0.7906 (tptp) REVERT: D 623 PHE cc_start: 0.7437 (m-80) cc_final: 0.7091 (m-80) REVERT: D 676 PHE cc_start: 0.8443 (t80) cc_final: 0.8227 (t80) REVERT: D 691 SER cc_start: 0.8830 (m) cc_final: 0.8525 (p) REVERT: D 703 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7819 (ttt90) REVERT: D 746 VAL cc_start: 0.9077 (t) cc_final: 0.8862 (m) REVERT: D 754 TYR cc_start: 0.9173 (m-10) cc_final: 0.8784 (m-80) REVERT: D 759 GLN cc_start: 0.8936 (mm110) cc_final: 0.8482 (mm110) REVERT: D 767 VAL cc_start: 0.8718 (m) cc_final: 0.8515 (m) REVERT: D 773 GLU cc_start: 0.7780 (mp0) cc_final: 0.7539 (mp0) REVERT: D 833 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8717 (tptp) REVERT: D 856 LYS cc_start: 0.8700 (tppt) cc_final: 0.8348 (tptp) REVERT: D 871 MET cc_start: 0.8158 (tmm) cc_final: 0.7957 (tpt) outliers start: 4 outliers final: 1 residues processed: 520 average time/residue: 0.1128 time to fit residues: 81.4407 Evaluate side-chains 284 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 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 549 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS B 549 ASN B 554 ASN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 554 ASN C 563 ASN C 704 GLN C 725 GLN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN D 554 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071818 restraints weight = 50032.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074059 restraints weight = 32514.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.075667 restraints weight = 23826.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.076760 restraints weight = 18830.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.077704 restraints weight = 15867.961| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12072 Z= 0.163 Angle : 0.728 12.242 16456 Z= 0.373 Chirality : 0.049 0.367 1898 Planarity : 0.006 0.051 2072 Dihedral : 10.440 78.803 1766 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.79 % 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 are not related in a simple way. whole: -3.20 (0.19), residues: 1452 helix: -1.90 (0.15), residues: 726 sheet: -2.40 (0.36), residues: 176 loop : -2.06 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 832 TYR 0.011 0.001 TYR A 552 PHE 0.028 0.002 PHE D 626 TRP 0.014 0.002 TRP A 878 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00349 (12060) covalent geometry : angle 0.70240 (16424) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.15060 ( 8) hydrogen bonds : bond 0.05518 ( 482) hydrogen bonds : angle 5.56198 ( 1464) link_BETA1-4 : bond 0.01394 ( 4) link_BETA1-4 : angle 3.25336 ( 12) link_NAG-ASN : bond 0.01524 ( 4) link_NAG-ASN : angle 6.29609 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 PHE cc_start: 0.7584 (t80) cc_final: 0.7027 (t80) REVERT: A 680 ILE cc_start: 0.9183 (mm) cc_final: 0.8956 (mm) REVERT: A 695 SER cc_start: 0.9123 (m) cc_final: 0.8884 (t) REVERT: A 749 LYS cc_start: 0.7530 (ptmt) cc_final: 0.7266 (ptpt) REVERT: A 754 TYR cc_start: 0.8380 (m-10) cc_final: 0.7878 (m-80) REVERT: A 772 ASP cc_start: 0.8646 (m-30) cc_final: 0.8402 (t70) REVERT: A 807 ASP cc_start: 0.8460 (t0) cc_final: 0.8242 (t0) REVERT: A 829 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8465 (mmmm) REVERT: A 850 ASP cc_start: 0.5931 (t0) cc_final: 0.5329 (t70) REVERT: B 564 PHE cc_start: 0.8189 (m-80) cc_final: 0.7901 (m-10) REVERT: B 599 LYS cc_start: 0.6889 (ptpp) cc_final: 0.6611 (mtpt) REVERT: B 610 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8244 (tptp) REVERT: B 612 PHE cc_start: 0.7699 (m-80) cc_final: 0.7129 (m-80) REVERT: B 617 TRP cc_start: 0.7615 (m100) cc_final: 0.7229 (m100) REVERT: B 689 ASN cc_start: 0.8726 (t0) cc_final: 0.8460 (t0) REVERT: B 692 TYR cc_start: 0.8541 (t80) cc_final: 0.8196 (t80) REVERT: B 700 LEU cc_start: 0.9123 (mm) cc_final: 0.8722 (mm) REVERT: B 767 VAL cc_start: 0.8671 (m) cc_final: 0.8410 (m) REVERT: B 772 ASP cc_start: 0.7828 (m-30) cc_final: 0.7342 (m-30) REVERT: B 814 MET cc_start: 0.8992 (mmp) cc_final: 0.8771 (mmm) REVERT: B 828 GLU cc_start: 0.8735 (mp0) cc_final: 0.8530 (mp0) REVERT: C 513 ASN cc_start: 0.8331 (m-40) cc_final: 0.7402 (p0) REVERT: C 630 MET cc_start: 0.7841 (mpp) cc_final: 0.7420 (mpp) REVERT: C 675 ARG cc_start: 0.4829 (mtt180) cc_final: 0.4212 (mtt180) REVERT: C 688 ILE cc_start: 0.9285 (mm) cc_final: 0.9038 (tp) REVERT: C 750 ASP cc_start: 0.6898 (p0) cc_final: 0.5674 (t70) REVERT: C 751 GLU cc_start: 0.8217 (pt0) cc_final: 0.7486 (pm20) REVERT: C 754 TYR cc_start: 0.7931 (m-10) cc_final: 0.7399 (m-80) REVERT: C 773 GLU cc_start: 0.8307 (mp0) cc_final: 0.7871 (mp0) REVERT: C 779 VAL cc_start: 0.9266 (t) cc_final: 0.8979 (t) REVERT: D 570 ASP cc_start: 0.7609 (m-30) cc_final: 0.7281 (m-30) REVERT: D 608 PHE cc_start: 0.5991 (t80) cc_final: 0.5418 (t80) REVERT: D 610 LYS cc_start: 0.8475 (ttpt) cc_final: 0.7880 (tptp) REVERT: D 612 PHE cc_start: 0.7664 (m-10) cc_final: 0.7129 (m-80) REVERT: D 676 PHE cc_start: 0.8588 (t80) cc_final: 0.8090 (t80) REVERT: D 722 ILE cc_start: 0.8884 (mt) cc_final: 0.8662 (mp) REVERT: D 754 TYR cc_start: 0.9097 (m-10) cc_final: 0.8622 (m-80) REVERT: D 772 ASP cc_start: 0.7799 (m-30) cc_final: 0.7450 (m-30) REVERT: D 837 TYR cc_start: 0.6078 (m-10) cc_final: 0.5750 (m-80) outliers start: 2 outliers final: 0 residues processed: 373 average time/residue: 0.1050 time to fit residues: 56.9248 Evaluate side-chains 247 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 125 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 133 optimal weight: 0.0670 chunk 92 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070378 restraints weight = 50281.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072635 restraints weight = 32082.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074214 restraints weight = 23203.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075406 restraints weight = 18258.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076136 restraints weight = 15187.819| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12072 Z= 0.158 Angle : 0.733 15.828 16456 Z= 0.365 Chirality : 0.049 0.582 1898 Planarity : 0.005 0.050 2072 Dihedral : 8.791 58.228 1766 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.16 % Allowed : 3.73 % Favored : 96.11 % 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 are not related in a simple way. whole: -2.34 (0.20), residues: 1452 helix: -1.05 (0.17), residues: 734 sheet: -2.14 (0.37), residues: 178 loop : -1.82 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 832 TYR 0.018 0.002 TYR C 552 PHE 0.020 0.002 PHE D 626 TRP 0.015 0.001 TRP B 485 HIS 0.003 0.001 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00344 (12060) covalent geometry : angle 0.69914 (16424) SS BOND : bond 0.00196 ( 4) SS BOND : angle 1.80264 ( 8) hydrogen bonds : bond 0.04604 ( 482) hydrogen bonds : angle 5.11158 ( 1464) link_BETA1-4 : bond 0.01206 ( 4) link_BETA1-4 : angle 3.51482 ( 12) link_NAG-ASN : bond 0.02349 ( 4) link_NAG-ASN : angle 7.28127 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 316 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 ILE cc_start: 0.9154 (mm) cc_final: 0.8951 (mm) REVERT: A 681 TRP cc_start: 0.8766 (t60) cc_final: 0.8559 (t60) REVERT: A 749 LYS cc_start: 0.7603 (ptmt) cc_final: 0.7335 (ptpt) REVERT: A 754 TYR cc_start: 0.8447 (m-10) cc_final: 0.7993 (m-80) REVERT: A 850 ASP cc_start: 0.5887 (t0) cc_final: 0.5516 (t0) REVERT: B 564 PHE cc_start: 0.8140 (m-80) cc_final: 0.7930 (m-10) REVERT: B 599 LYS cc_start: 0.6768 (ptpp) cc_final: 0.6434 (mmmt) REVERT: B 610 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8241 (tptp) REVERT: B 612 PHE cc_start: 0.7659 (m-80) cc_final: 0.7439 (m-80) REVERT: B 624 PHE cc_start: 0.7556 (t80) cc_final: 0.7351 (t80) REVERT: B 692 TYR cc_start: 0.8690 (t80) cc_final: 0.8489 (t80) REVERT: B 700 LEU cc_start: 0.9102 (mm) cc_final: 0.8731 (mm) REVERT: B 772 ASP cc_start: 0.7905 (m-30) cc_final: 0.7415 (m-30) REVERT: B 823 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 828 GLU cc_start: 0.8714 (mp0) cc_final: 0.8480 (mp0) REVERT: C 513 ASN cc_start: 0.8420 (m-40) cc_final: 0.7542 (p0) REVERT: C 562 ASP cc_start: 0.8028 (t0) cc_final: 0.7640 (t0) REVERT: C 616 MET cc_start: 0.8203 (tpp) cc_final: 0.7975 (tpp) REVERT: C 630 MET cc_start: 0.7915 (mpp) cc_final: 0.7433 (mpp) REVERT: C 675 ARG cc_start: 0.4948 (mtt180) cc_final: 0.4371 (mtt180) REVERT: C 681 TRP cc_start: 0.8191 (t60) cc_final: 0.7898 (t60) REVERT: C 688 ILE cc_start: 0.9309 (mm) cc_final: 0.9065 (tp) REVERT: C 709 ILE cc_start: 0.7977 (mm) cc_final: 0.7510 (mm) REVERT: C 751 GLU cc_start: 0.8337 (pt0) cc_final: 0.7791 (pm20) REVERT: C 754 TYR cc_start: 0.7987 (m-10) cc_final: 0.7518 (m-80) REVERT: C 779 VAL cc_start: 0.9264 (t) cc_final: 0.9049 (t) REVERT: D 570 ASP cc_start: 0.7528 (m-30) cc_final: 0.7199 (m-30) REVERT: D 608 PHE cc_start: 0.5559 (t80) cc_final: 0.5021 (t80) REVERT: D 610 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7809 (tptp) REVERT: D 676 PHE cc_start: 0.8618 (t80) cc_final: 0.8373 (t80) REVERT: D 722 ILE cc_start: 0.8964 (mt) cc_final: 0.8728 (mp) REVERT: D 772 ASP cc_start: 0.7750 (m-30) cc_final: 0.7496 (m-30) REVERT: D 814 MET cc_start: 0.8633 (mmp) cc_final: 0.8432 (mmm) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.0949 time to fit residues: 45.5274 Evaluate side-chains 224 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 86 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 40 optimal weight: 0.0020 chunk 124 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 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 = 0.3602 r_free = 0.3602 target = 0.088275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070492 restraints weight = 51448.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072656 restraints weight = 33468.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074186 restraints weight = 24652.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.075227 restraints weight = 19602.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076086 restraints weight = 16553.552| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12072 Z= 0.141 Angle : 0.678 13.169 16456 Z= 0.341 Chirality : 0.048 0.426 1898 Planarity : 0.004 0.043 2072 Dihedral : 7.239 44.343 1766 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.22 % 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 are not related in a simple way. whole: -1.66 (0.21), residues: 1452 helix: -0.40 (0.18), residues: 730 sheet: -1.91 (0.40), residues: 172 loop : -1.63 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 495 TYR 0.017 0.001 TYR C 520 PHE 0.021 0.002 PHE D 626 TRP 0.015 0.001 TRP D 681 HIS 0.002 0.001 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00305 (12060) covalent geometry : angle 0.64870 (16424) SS BOND : bond 0.00460 ( 4) SS BOND : angle 1.77546 ( 8) hydrogen bonds : bond 0.03930 ( 482) hydrogen bonds : angle 4.83670 ( 1464) link_BETA1-4 : bond 0.01169 ( 4) link_BETA1-4 : angle 3.33950 ( 12) link_NAG-ASN : bond 0.01518 ( 4) link_NAG-ASN : angle 6.35821 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 681 TRP cc_start: 0.8712 (t60) cc_final: 0.8472 (t60) REVERT: A 749 LYS cc_start: 0.7729 (ptmt) cc_final: 0.7329 (ptpt) REVERT: A 754 TYR cc_start: 0.8425 (m-10) cc_final: 0.7895 (m-80) REVERT: A 793 GLN cc_start: 0.5724 (tp40) cc_final: 0.5205 (tp40) REVERT: A 850 ASP cc_start: 0.5868 (t0) cc_final: 0.5485 (t0) REVERT: B 570 ASP cc_start: 0.7046 (m-30) cc_final: 0.6614 (m-30) REVERT: B 572 THR cc_start: 0.8954 (m) cc_final: 0.8413 (p) REVERT: B 599 LYS cc_start: 0.7023 (ptpp) cc_final: 0.6554 (mtpt) REVERT: B 610 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8179 (tptp) REVERT: B 624 PHE cc_start: 0.7535 (t80) cc_final: 0.7334 (t80) REVERT: B 700 LEU cc_start: 0.9118 (mm) cc_final: 0.8782 (mm) REVERT: B 828 GLU cc_start: 0.8650 (mp0) cc_final: 0.8425 (mp0) REVERT: B 835 LEU cc_start: 0.8438 (mt) cc_final: 0.8186 (mt) REVERT: B 837 TYR cc_start: 0.5901 (m-10) cc_final: 0.5518 (m-80) REVERT: C 513 ASN cc_start: 0.8476 (m-40) cc_final: 0.7590 (p0) REVERT: C 630 MET cc_start: 0.7969 (mpp) cc_final: 0.7481 (mpp) REVERT: C 675 ARG cc_start: 0.4763 (mtt180) cc_final: 0.4136 (mtt180) REVERT: C 681 TRP cc_start: 0.8262 (t60) cc_final: 0.7995 (t60) REVERT: C 709 ILE cc_start: 0.8026 (mm) cc_final: 0.7573 (mm) REVERT: C 751 GLU cc_start: 0.8335 (pt0) cc_final: 0.7859 (pm20) REVERT: C 754 TYR cc_start: 0.7852 (m-10) cc_final: 0.7493 (m-80) REVERT: C 779 VAL cc_start: 0.9285 (t) cc_final: 0.9009 (p) REVERT: C 843 MET cc_start: 0.5969 (tmm) cc_final: 0.5638 (tmm) REVERT: D 608 PHE cc_start: 0.5474 (t80) cc_final: 0.4913 (t80) REVERT: D 610 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7768 (tptp) REVERT: D 676 PHE cc_start: 0.8615 (t80) cc_final: 0.8371 (t80) REVERT: D 754 TYR cc_start: 0.8763 (m-80) cc_final: 0.8544 (m-80) REVERT: D 772 ASP cc_start: 0.7687 (m-30) cc_final: 0.7316 (m-30) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.0938 time to fit residues: 42.7659 Evaluate side-chains 214 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 85 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.088011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069875 restraints weight = 50430.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072085 restraints weight = 32499.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073639 restraints weight = 23718.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.074789 restraints weight = 18768.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075675 restraints weight = 15677.901| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12072 Z= 0.132 Angle : 0.663 12.617 16456 Z= 0.333 Chirality : 0.049 0.786 1898 Planarity : 0.004 0.044 2072 Dihedral : 6.772 44.048 1766 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.16 % Allowed : 1.90 % Favored : 97.94 % 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 are not related in a simple way. whole: -1.39 (0.21), residues: 1452 helix: -0.10 (0.19), residues: 742 sheet: -1.74 (0.39), residues: 182 loop : -1.65 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 495 TYR 0.018 0.002 TYR B 692 PHE 0.019 0.001 PHE D 626 TRP 0.014 0.001 TRP D 681 HIS 0.017 0.002 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00288 (12060) covalent geometry : angle 0.63120 (16424) SS BOND : bond 0.00128 ( 4) SS BOND : angle 1.25700 ( 8) hydrogen bonds : bond 0.03618 ( 482) hydrogen bonds : angle 4.62429 ( 1464) link_BETA1-4 : bond 0.01065 ( 4) link_BETA1-4 : angle 3.67180 ( 12) link_NAG-ASN : bond 0.01334 ( 4) link_NAG-ASN : angle 6.58089 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 ILE cc_start: 0.9174 (mm) cc_final: 0.8955 (mm) REVERT: A 681 TRP cc_start: 0.8680 (t60) cc_final: 0.8475 (t60) REVERT: A 749 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7551 (ptpt) REVERT: A 754 TYR cc_start: 0.8461 (m-10) cc_final: 0.7926 (m-80) REVERT: A 850 ASP cc_start: 0.5798 (t0) cc_final: 0.5573 (t0) REVERT: A 855 LEU cc_start: 0.7672 (mm) cc_final: 0.7420 (tp) REVERT: B 572 THR cc_start: 0.8991 (m) cc_final: 0.8398 (p) REVERT: B 599 LYS cc_start: 0.7122 (ptpp) cc_final: 0.6681 (mmmt) REVERT: B 612 PHE cc_start: 0.7429 (m-80) cc_final: 0.7099 (m-80) REVERT: B 617 TRP cc_start: 0.7079 (m100) cc_final: 0.4799 (t-100) REVERT: B 685 VAL cc_start: 0.8805 (t) cc_final: 0.8582 (t) REVERT: B 700 LEU cc_start: 0.9102 (mm) cc_final: 0.8786 (mm) REVERT: B 798 THR cc_start: 0.9121 (t) cc_final: 0.8909 (m) REVERT: B 828 GLU cc_start: 0.8736 (mp0) cc_final: 0.8512 (mp0) REVERT: C 562 ASP cc_start: 0.8254 (t0) cc_final: 0.7814 (t70) REVERT: C 620 THR cc_start: 0.8386 (m) cc_final: 0.8171 (p) REVERT: C 630 MET cc_start: 0.8017 (mpp) cc_final: 0.7517 (mpp) REVERT: C 675 ARG cc_start: 0.4724 (mtt180) cc_final: 0.4210 (mtt180) REVERT: C 681 TRP cc_start: 0.8264 (t60) cc_final: 0.8002 (t60) REVERT: C 691 SER cc_start: 0.9008 (m) cc_final: 0.8791 (p) REVERT: C 709 ILE cc_start: 0.8119 (mm) cc_final: 0.7625 (mm) REVERT: C 751 GLU cc_start: 0.8433 (pt0) cc_final: 0.7936 (pm20) REVERT: C 754 TYR cc_start: 0.7803 (m-10) cc_final: 0.7543 (m-80) REVERT: D 608 PHE cc_start: 0.5402 (t80) cc_final: 0.4931 (t80) REVERT: D 610 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7755 (tptp) REVERT: D 676 PHE cc_start: 0.8649 (t80) cc_final: 0.8421 (t80) REVERT: D 828 GLU cc_start: 0.8253 (pm20) cc_final: 0.8042 (pm20) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.0930 time to fit residues: 42.2405 Evaluate side-chains 224 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 119 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 725 GLN B 805 GLN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071212 restraints weight = 52023.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073432 restraints weight = 33872.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074973 restraints weight = 24890.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.076030 restraints weight = 19822.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076855 restraints weight = 16784.489| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12072 Z= 0.124 Angle : 0.645 12.296 16456 Z= 0.324 Chirality : 0.047 0.522 1898 Planarity : 0.004 0.046 2072 Dihedral : 6.644 48.168 1766 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.32 % Allowed : 2.46 % Favored : 97.22 % 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 are not related in a simple way. whole: -1.05 (0.22), residues: 1452 helix: 0.22 (0.19), residues: 728 sheet: -1.59 (0.40), residues: 182 loop : -1.53 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 495 TYR 0.015 0.001 TYR D 776 PHE 0.036 0.001 PHE B 564 TRP 0.009 0.001 TRP C 632 HIS 0.001 0.000 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00274 (12060) covalent geometry : angle 0.61590 (16424) SS BOND : bond 0.00091 ( 4) SS BOND : angle 1.66198 ( 8) hydrogen bonds : bond 0.03405 ( 482) hydrogen bonds : angle 4.54041 ( 1464) link_BETA1-4 : bond 0.01135 ( 4) link_BETA1-4 : angle 3.20835 ( 12) link_NAG-ASN : bond 0.01485 ( 4) link_NAG-ASN : angle 6.22552 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 278 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 MET cc_start: 0.6926 (mmt) cc_final: 0.6723 (tpp) REVERT: A 626 PHE cc_start: 0.7767 (t80) cc_final: 0.7560 (t80) REVERT: A 675 ARG cc_start: 0.6033 (mtt180) cc_final: 0.5768 (mtt180) REVERT: A 749 LYS cc_start: 0.7855 (ptmt) cc_final: 0.7518 (ptpt) REVERT: A 754 TYR cc_start: 0.8457 (m-10) cc_final: 0.7900 (m-80) REVERT: B 496 ILE cc_start: 0.8861 (mt) cc_final: 0.8619 (mt) REVERT: B 572 THR cc_start: 0.8979 (m) cc_final: 0.8483 (p) REVERT: B 599 LYS cc_start: 0.7181 (ptpp) cc_final: 0.6665 (mmmt) REVERT: B 610 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8456 (mtpp) REVERT: B 612 PHE cc_start: 0.7516 (m-80) cc_final: 0.7292 (m-80) REVERT: B 617 TRP cc_start: 0.7099 (m100) cc_final: 0.4792 (t-100) REVERT: B 700 LEU cc_start: 0.9126 (mm) cc_final: 0.8860 (mm) REVERT: B 828 GLU cc_start: 0.8711 (mp0) cc_final: 0.8504 (mp0) REVERT: C 562 ASP cc_start: 0.8289 (t0) cc_final: 0.7828 (t70) REVERT: C 592 LEU cc_start: 0.9282 (mt) cc_final: 0.8782 (mt) REVERT: C 620 THR cc_start: 0.8275 (m) cc_final: 0.8074 (p) REVERT: C 630 MET cc_start: 0.8038 (mpp) cc_final: 0.7550 (mpp) REVERT: C 675 ARG cc_start: 0.4799 (mtt180) cc_final: 0.4300 (mtt180) REVERT: C 681 TRP cc_start: 0.8280 (t60) cc_final: 0.8039 (t60) REVERT: C 691 SER cc_start: 0.9029 (m) cc_final: 0.8797 (p) REVERT: C 709 ILE cc_start: 0.8194 (mm) cc_final: 0.7733 (mm) REVERT: C 751 GLU cc_start: 0.8367 (pt0) cc_final: 0.7920 (pm20) REVERT: C 754 TYR cc_start: 0.7795 (m-10) cc_final: 0.7546 (m-80) REVERT: D 608 PHE cc_start: 0.5325 (t80) cc_final: 0.4669 (t80) REVERT: D 610 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7712 (tptp) REVERT: D 676 PHE cc_start: 0.8610 (t80) cc_final: 0.8273 (t80) REVERT: D 828 GLU cc_start: 0.8237 (pm20) cc_final: 0.7967 (pm20) REVERT: D 832 ARG cc_start: 0.8284 (mpp80) cc_final: 0.7694 (ptp-110) REVERT: D 879 ARG cc_start: 0.6785 (tpt-90) cc_final: 0.6404 (mmt90) outliers start: 4 outliers final: 1 residues processed: 282 average time/residue: 0.0934 time to fit residues: 40.0271 Evaluate side-chains 225 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 GLN B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068935 restraints weight = 51233.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071063 restraints weight = 32958.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072554 restraints weight = 24111.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073610 restraints weight = 19124.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074271 restraints weight = 16118.369| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12072 Z= 0.168 Angle : 0.691 12.062 16456 Z= 0.349 Chirality : 0.052 1.024 1898 Planarity : 0.005 0.044 2072 Dihedral : 6.622 46.346 1766 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.08 % Allowed : 1.83 % Favored : 98.10 % 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 are not related in a simple way. whole: -1.05 (0.22), residues: 1452 helix: 0.26 (0.19), residues: 740 sheet: -1.67 (0.40), residues: 182 loop : -1.59 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 495 TYR 0.017 0.002 TYR C 552 PHE 0.028 0.002 PHE D 564 TRP 0.013 0.001 TRP A 859 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00375 (12060) covalent geometry : angle 0.65823 (16424) SS BOND : bond 0.00252 ( 4) SS BOND : angle 1.71772 ( 8) hydrogen bonds : bond 0.03486 ( 482) hydrogen bonds : angle 4.63187 ( 1464) link_BETA1-4 : bond 0.01107 ( 4) link_BETA1-4 : angle 3.50250 ( 12) link_NAG-ASN : bond 0.01821 ( 4) link_NAG-ASN : angle 6.89764 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ASP cc_start: 0.8306 (m-30) cc_final: 0.7685 (m-30) REVERT: A 626 PHE cc_start: 0.7752 (t80) cc_final: 0.7450 (t80) REVERT: A 680 ILE cc_start: 0.9218 (mm) cc_final: 0.9007 (mm) REVERT: A 749 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7504 (ptpt) REVERT: A 754 TYR cc_start: 0.8385 (m-10) cc_final: 0.7808 (m-80) REVERT: A 855 LEU cc_start: 0.7558 (mm) cc_final: 0.7337 (tp) REVERT: B 599 LYS cc_start: 0.7225 (ptpp) cc_final: 0.6610 (mmmt) REVERT: B 608 PHE cc_start: 0.6442 (t80) cc_final: 0.6215 (t80) REVERT: B 610 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8527 (mtpp) REVERT: B 612 PHE cc_start: 0.7668 (m-80) cc_final: 0.7367 (m-80) REVERT: B 617 TRP cc_start: 0.7201 (m100) cc_final: 0.4998 (t-100) REVERT: B 700 LEU cc_start: 0.9194 (mm) cc_final: 0.8948 (mm) REVERT: B 828 GLU cc_start: 0.8761 (mp0) cc_final: 0.8547 (mp0) REVERT: B 858 PHE cc_start: 0.6681 (p90) cc_final: 0.6042 (p90) REVERT: C 562 ASP cc_start: 0.8397 (t0) cc_final: 0.8169 (t70) REVERT: C 585 GLN cc_start: 0.9244 (tp40) cc_final: 0.8883 (mm-40) REVERT: C 630 MET cc_start: 0.8081 (mpp) cc_final: 0.7489 (mpp) REVERT: C 632 TRP cc_start: 0.6680 (t60) cc_final: 0.6462 (t60) REVERT: C 675 ARG cc_start: 0.5181 (mtt180) cc_final: 0.4861 (mtt180) REVERT: C 681 TRP cc_start: 0.8272 (t60) cc_final: 0.7665 (t60) REVERT: C 695 SER cc_start: 0.9011 (m) cc_final: 0.8690 (t) REVERT: C 709 ILE cc_start: 0.8152 (mm) cc_final: 0.7916 (mm) REVERT: D 610 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7780 (tptp) REVERT: D 676 PHE cc_start: 0.8578 (t80) cc_final: 0.8320 (t80) REVERT: D 814 MET cc_start: 0.8933 (mmp) cc_final: 0.8704 (mmp) REVERT: D 828 GLU cc_start: 0.8313 (pm20) cc_final: 0.8078 (pm20) REVERT: D 879 ARG cc_start: 0.6816 (tpt-90) cc_final: 0.6417 (mmt90) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.0906 time to fit residues: 37.0836 Evaluate side-chains 213 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 0.0020 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN D 820 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070148 restraints weight = 51460.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072296 restraints weight = 33045.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073847 restraints weight = 24282.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074835 restraints weight = 19292.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075675 restraints weight = 16355.156| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12072 Z= 0.125 Angle : 0.665 12.121 16456 Z= 0.330 Chirality : 0.049 0.730 1898 Planarity : 0.004 0.045 2072 Dihedral : 6.549 49.172 1766 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.16 % Allowed : 0.71 % Favored : 99.13 % 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 are not related in a simple way. whole: -0.80 (0.22), residues: 1452 helix: 0.50 (0.19), residues: 730 sheet: -1.58 (0.40), residues: 182 loop : -1.50 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 495 TYR 0.017 0.001 TYR D 776 PHE 0.033 0.001 PHE C 624 TRP 0.011 0.001 TRP D 681 HIS 0.001 0.000 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00281 (12060) covalent geometry : angle 0.63427 (16424) SS BOND : bond 0.00200 ( 4) SS BOND : angle 2.36461 ( 8) hydrogen bonds : bond 0.03269 ( 482) hydrogen bonds : angle 4.49822 ( 1464) link_BETA1-4 : bond 0.01047 ( 4) link_BETA1-4 : angle 3.11156 ( 12) link_NAG-ASN : bond 0.01677 ( 4) link_NAG-ASN : angle 6.53162 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7273 (m-80) cc_final: 0.6766 (m-80) REVERT: A 570 ASP cc_start: 0.8109 (m-30) cc_final: 0.7509 (m-30) REVERT: A 626 PHE cc_start: 0.7711 (t80) cc_final: 0.7369 (t80) REVERT: A 675 ARG cc_start: 0.6328 (mtt180) cc_final: 0.5460 (mtm-85) REVERT: A 749 LYS cc_start: 0.7828 (ptmt) cc_final: 0.7486 (ptpt) REVERT: A 754 TYR cc_start: 0.8422 (m-10) cc_final: 0.7808 (m-80) REVERT: B 599 LYS cc_start: 0.7177 (ptpp) cc_final: 0.6581 (mmmt) REVERT: B 608 PHE cc_start: 0.6518 (t80) cc_final: 0.6227 (t80) REVERT: B 610 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8491 (mtpp) REVERT: B 612 PHE cc_start: 0.7718 (m-80) cc_final: 0.7385 (m-80) REVERT: B 617 TRP cc_start: 0.7175 (m100) cc_final: 0.5021 (t-100) REVERT: B 630 MET cc_start: 0.7503 (ppp) cc_final: 0.7182 (ppp) REVERT: B 700 LEU cc_start: 0.9250 (mm) cc_final: 0.8929 (mm) REVERT: B 828 GLU cc_start: 0.8764 (mp0) cc_final: 0.8554 (mp0) REVERT: B 856 LYS cc_start: 0.8045 (tptt) cc_final: 0.7328 (tptt) REVERT: C 532 LEU cc_start: 0.9120 (mt) cc_final: 0.8073 (tp) REVERT: C 534 TYR cc_start: 0.6440 (m-10) cc_final: 0.6236 (m-10) REVERT: C 562 ASP cc_start: 0.8386 (t0) cc_final: 0.8172 (t70) REVERT: C 630 MET cc_start: 0.8140 (mpp) cc_final: 0.7675 (mpp) REVERT: C 675 ARG cc_start: 0.5042 (mtt180) cc_final: 0.4698 (mtt180) REVERT: C 695 SER cc_start: 0.8913 (m) cc_final: 0.8646 (t) REVERT: C 709 ILE cc_start: 0.8214 (mm) cc_final: 0.7965 (mm) REVERT: D 610 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7756 (tptp) REVERT: D 676 PHE cc_start: 0.8613 (t80) cc_final: 0.8272 (t80) REVERT: D 814 MET cc_start: 0.8893 (mmp) cc_final: 0.8667 (mmp) REVERT: D 828 GLU cc_start: 0.8318 (pm20) cc_final: 0.8011 (pm20) REVERT: D 832 ARG cc_start: 0.8309 (mpp80) cc_final: 0.7684 (ptp-110) REVERT: D 879 ARG cc_start: 0.6742 (tpt-90) cc_final: 0.6305 (mmt90) outliers start: 2 outliers final: 0 residues processed: 282 average time/residue: 0.0991 time to fit residues: 41.9193 Evaluate side-chains 210 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 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 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 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 = 0.3590 r_free = 0.3590 target = 0.087798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070084 restraints weight = 50252.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072248 restraints weight = 32092.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073798 restraints weight = 23514.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074898 restraints weight = 18633.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075673 restraints weight = 15666.930| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12072 Z= 0.131 Angle : 0.665 12.183 16456 Z= 0.332 Chirality : 0.048 0.625 1898 Planarity : 0.004 0.044 2072 Dihedral : 6.448 48.038 1766 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 are not related in a simple way. whole: -0.72 (0.22), residues: 1452 helix: 0.54 (0.19), residues: 734 sheet: -1.49 (0.40), residues: 180 loop : -1.44 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 708 TYR 0.015 0.001 TYR D 776 PHE 0.019 0.001 PHE D 626 TRP 0.042 0.001 TRP D 617 HIS 0.011 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00295 (12060) covalent geometry : angle 0.63603 (16424) SS BOND : bond 0.00134 ( 4) SS BOND : angle 2.13207 ( 8) hydrogen bonds : bond 0.03223 ( 482) hydrogen bonds : angle 4.47910 ( 1464) link_BETA1-4 : bond 0.01032 ( 4) link_BETA1-4 : angle 3.00738 ( 12) link_NAG-ASN : bond 0.01585 ( 4) link_NAG-ASN : angle 6.41253 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7293 (m-80) cc_final: 0.6790 (m-80) REVERT: A 570 ASP cc_start: 0.8180 (m-30) cc_final: 0.7477 (m-30) REVERT: A 626 PHE cc_start: 0.7713 (t80) cc_final: 0.7342 (t80) REVERT: A 680 ILE cc_start: 0.9222 (mm) cc_final: 0.9012 (mm) REVERT: A 749 LYS cc_start: 0.7854 (ptmt) cc_final: 0.7496 (ptpt) REVERT: A 754 TYR cc_start: 0.8439 (m-10) cc_final: 0.7839 (m-80) REVERT: A 794 GLU cc_start: 0.6532 (mp0) cc_final: 0.5891 (mp0) REVERT: B 599 LYS cc_start: 0.7261 (ptpp) cc_final: 0.6586 (mmmt) REVERT: B 608 PHE cc_start: 0.6474 (t80) cc_final: 0.6207 (t80) REVERT: B 610 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8480 (mtpp) REVERT: B 612 PHE cc_start: 0.7688 (m-80) cc_final: 0.7420 (m-80) REVERT: B 617 TRP cc_start: 0.7202 (m100) cc_final: 0.5078 (t-100) REVERT: B 630 MET cc_start: 0.7568 (ppp) cc_final: 0.7255 (ppp) REVERT: B 700 LEU cc_start: 0.9084 (mm) cc_final: 0.8828 (mm) REVERT: B 828 GLU cc_start: 0.8771 (mp0) cc_final: 0.8550 (mp0) REVERT: B 856 LYS cc_start: 0.8122 (tptt) cc_final: 0.7527 (tptt) REVERT: C 562 ASP cc_start: 0.8507 (t0) cc_final: 0.8303 (t70) REVERT: C 630 MET cc_start: 0.8153 (mpp) cc_final: 0.7668 (mpp) REVERT: C 675 ARG cc_start: 0.5187 (mtt180) cc_final: 0.4842 (mtt180) REVERT: C 695 SER cc_start: 0.8978 (m) cc_final: 0.8658 (t) REVERT: C 704 GLN cc_start: 0.8958 (mp10) cc_final: 0.8671 (mp10) REVERT: C 709 ILE cc_start: 0.8230 (mm) cc_final: 0.7939 (mm) REVERT: D 676 PHE cc_start: 0.8591 (t80) cc_final: 0.8264 (t80) REVERT: D 814 MET cc_start: 0.8962 (mmp) cc_final: 0.8669 (mmp) REVERT: D 832 ARG cc_start: 0.8362 (mpp80) cc_final: 0.7705 (ptp-110) REVERT: D 879 ARG cc_start: 0.6722 (tpt-90) cc_final: 0.6305 (mmt90) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.0925 time to fit residues: 37.3329 Evaluate side-chains 212 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 125 optimal weight: 0.0870 chunk 28 optimal weight: 0.4980 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 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 = 0.3566 r_free = 0.3566 target = 0.086378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068480 restraints weight = 51548.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070712 restraints weight = 32606.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072229 restraints weight = 23641.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.073369 restraints weight = 18740.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074190 restraints weight = 15706.739| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12072 Z= 0.170 Angle : 0.697 12.092 16456 Z= 0.350 Chirality : 0.049 0.647 1898 Planarity : 0.005 0.045 2072 Dihedral : 6.488 46.209 1766 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 are not related in a simple way. whole: -0.78 (0.22), residues: 1452 helix: 0.54 (0.19), residues: 726 sheet: -1.60 (0.40), residues: 182 loop : -1.49 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 708 TYR 0.016 0.002 TYR C 552 PHE 0.021 0.002 PHE D 626 TRP 0.053 0.002 TRP D 617 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00383 (12060) covalent geometry : angle 0.66797 (16424) SS BOND : bond 0.00120 ( 4) SS BOND : angle 2.06192 ( 8) hydrogen bonds : bond 0.03380 ( 482) hydrogen bonds : angle 4.61676 ( 1464) link_BETA1-4 : bond 0.01129 ( 4) link_BETA1-4 : angle 3.11171 ( 12) link_NAG-ASN : bond 0.01593 ( 4) link_NAG-ASN : angle 6.58585 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7474 (m-80) cc_final: 0.6894 (m-80) REVERT: A 570 ASP cc_start: 0.8395 (m-30) cc_final: 0.7573 (m-30) REVERT: A 626 PHE cc_start: 0.7727 (t80) cc_final: 0.7410 (m-80) REVERT: A 749 LYS cc_start: 0.7905 (ptmt) cc_final: 0.7545 (ptpt) REVERT: A 754 TYR cc_start: 0.8405 (m-10) cc_final: 0.7671 (m-80) REVERT: A 794 GLU cc_start: 0.6508 (mp0) cc_final: 0.5882 (mp0) REVERT: B 599 LYS cc_start: 0.7417 (ptpp) cc_final: 0.6613 (mmmt) REVERT: B 610 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8484 (mtpp) REVERT: B 612 PHE cc_start: 0.7731 (m-80) cc_final: 0.7435 (m-80) REVERT: B 617 TRP cc_start: 0.7201 (m100) cc_final: 0.5182 (t-100) REVERT: B 630 MET cc_start: 0.7478 (ppp) cc_final: 0.7103 (ppp) REVERT: B 828 GLU cc_start: 0.8781 (mp0) cc_final: 0.8558 (mp0) REVERT: C 630 MET cc_start: 0.8153 (mpp) cc_final: 0.7550 (mpp) REVERT: C 675 ARG cc_start: 0.5707 (mtt180) cc_final: 0.5253 (mtt180) REVERT: C 695 SER cc_start: 0.9004 (m) cc_final: 0.8736 (t) REVERT: C 709 ILE cc_start: 0.8207 (mm) cc_final: 0.7977 (mm) REVERT: C 725 GLN cc_start: 0.7531 (mt0) cc_final: 0.7060 (mt0) REVERT: C 754 TYR cc_start: 0.7881 (m-80) cc_final: 0.7499 (m-80) REVERT: C 779 VAL cc_start: 0.9196 (t) cc_final: 0.8977 (t) REVERT: D 612 PHE cc_start: 0.7571 (m-10) cc_final: 0.7340 (m-10) REVERT: D 676 PHE cc_start: 0.8588 (t80) cc_final: 0.8346 (t80) REVERT: D 814 MET cc_start: 0.8937 (mmp) cc_final: 0.8725 (mmm) REVERT: D 879 ARG cc_start: 0.6702 (tpt-90) cc_final: 0.6265 (mmt90) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.0894 time to fit residues: 36.5744 Evaluate side-chains 206 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 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 = 0.3580 r_free = 0.3580 target = 0.087247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069321 restraints weight = 51511.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071582 restraints weight = 32345.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073128 restraints weight = 23421.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074244 restraints weight = 18566.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075020 restraints weight = 15634.704| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12072 Z= 0.137 Angle : 0.692 12.175 16456 Z= 0.343 Chirality : 0.048 0.591 1898 Planarity : 0.005 0.051 2072 Dihedral : 6.443 47.282 1766 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 are not related in a simple way. whole: -0.72 (0.22), residues: 1452 helix: 0.54 (0.19), residues: 730 sheet: -1.45 (0.40), residues: 180 loop : -1.45 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 495 TYR 0.015 0.002 TYR D 776 PHE 0.021 0.001 PHE D 626 TRP 0.050 0.001 TRP D 617 HIS 0.001 0.000 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00318 (12060) covalent geometry : angle 0.66435 (16424) SS BOND : bond 0.00087 ( 4) SS BOND : angle 1.93042 ( 8) hydrogen bonds : bond 0.03286 ( 482) hydrogen bonds : angle 4.53903 ( 1464) link_BETA1-4 : bond 0.01014 ( 4) link_BETA1-4 : angle 2.98425 ( 12) link_NAG-ASN : bond 0.01560 ( 4) link_NAG-ASN : angle 6.38951 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1984.03 seconds wall clock time: 35 minutes 7.64 seconds (2107.64 seconds total)