Starting phenix.real_space_refine on Fri Jul 3 04:01:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lzi_23607/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2026/7lzi_23607.cif" } 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-6108/lib/python3.11/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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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: 3.12, per 1000 atoms: 0.26 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: 1.19 Conformation dependent library (CDL) restraints added in 387.2 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: 0.27 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: 1.39 Time building geometry restraints manager: 1.51 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 - 14.72: 6555 14.72 - 29.44: 352 29.44 - 44.16: 93 44.16 - 58.88: 16 58.88 - 73.60: 12 Dihedral angle restraints: 7028 sinusoidal: 2742 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 7025 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: 4.920 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 10.790 73.597 4248 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/Z covalent geometry : bond 0.00484 / 0.25 (12060) covalent geometry : angle 0.94027 / 0.53 (16424) SS BOND : bond 0.00122 / 0.06 ( 4) SS BOND : angle 2.12299 / 1.41 ( 8) hydrogen bonds : bond 0.29658 / 19.94 ( 482) hydrogen bonds : angle 9.39239 / 6.69 ( 1464) link_BETA1-4 : bond 0.02179 / 1.11 ( 4) link_BETA1-4 : angle 4.47426 / 2.24 ( 12) link_NAG-ASN : bond 0.03804 / 1.94 ( 4) link_NAG-ASN : angle 8.57110 / 6.04 ( 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 : 0.354 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: 0.0967 time to fit residues: 70.7202 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 : 0.291 ------------------------------------------------------------------------------- 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... 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 = 0.3618 r_free = 0.3618 target = 0.089608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071371 restraints weight = 48895.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073627 restraints weight = 31541.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075263 restraints weight = 23014.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076464 restraints weight = 18109.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.077390 restraints weight = 15058.314| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12072 Z= 0.164 Angle : 0.716 12.834 16456 Z= 0.373 Chirality : 0.048 0.294 1898 Planarity : 0.006 0.050 2072 Dihedral : 5.863 25.419 1598 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.16 % Allowed : 3.81 % Favored : 96.03 % 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: -3.29 (0.19), residues: 1452 helix: -1.98 (0.15), residues: 728 sheet: -2.42 (0.36), residues: 176 loop : -2.10 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 832 TYR 0.012 0.001 TYR A 552 PHE 0.026 0.002 PHE D 626 TRP 0.016 0.002 TRP A 878 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (12060) covalent geometry : angle 0.69302 / 0.37 (16424) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 1.16143 / 0.73 ( 8) hydrogen bonds : bond 0.05920 / 3.89 ( 482) hydrogen bonds : angle 5.70188 / 4.07 ( 1464) link_BETA1-4 : bond 0.00785 / 0.39 ( 4) link_BETA1-4 : angle 2.24848 / 1.16 ( 12) link_NAG-ASN : bond 0.01780 / 0.91 ( 4) link_NAG-ASN : angle 6.25583 / 4.17 ( 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 373 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.384 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 626 PHE cc_start: 0.7558 (t80) cc_final: 0.6974 (t80) REVERT: A 680 ILE cc_start: 0.9195 (mm) cc_final: 0.8975 (mm) REVERT: A 695 SER cc_start: 0.9138 (m) cc_final: 0.8885 (t) REVERT: A 713 ASP cc_start: 0.8799 (m-30) cc_final: 0.8381 (p0) REVERT: A 722 ILE cc_start: 0.8675 (mt) cc_final: 0.8468 (tt) REVERT: A 749 LYS cc_start: 0.7513 (ptmt) cc_final: 0.7252 (ptpt) REVERT: A 754 TYR cc_start: 0.8385 (m-10) cc_final: 0.7882 (m-80) REVERT: A 772 ASP cc_start: 0.8641 (m-30) cc_final: 0.8394 (t70) REVERT: A 807 ASP cc_start: 0.8493 (t0) cc_final: 0.8248 (t0) REVERT: A 814 MET cc_start: 0.9030 (mtp) cc_final: 0.8788 (mtp) REVERT: A 829 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8491 (mmmm) REVERT: B 564 PHE cc_start: 0.8242 (m-80) cc_final: 0.7933 (m-10) REVERT: B 599 LYS cc_start: 0.6888 (ptpp) cc_final: 0.6613 (mtpt) REVERT: B 610 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8298 (tptp) REVERT: B 612 PHE cc_start: 0.7655 (m-80) cc_final: 0.7061 (m-80) REVERT: B 617 TRP cc_start: 0.7625 (m100) cc_final: 0.7192 (m100) REVERT: B 689 ASN cc_start: 0.8722 (t0) cc_final: 0.8450 (t0) REVERT: B 692 TYR cc_start: 0.8549 (t80) cc_final: 0.8209 (t80) REVERT: B 700 LEU cc_start: 0.9108 (mm) cc_final: 0.8711 (mm) REVERT: B 767 VAL cc_start: 0.8676 (m) cc_final: 0.8422 (m) REVERT: B 772 ASP cc_start: 0.7869 (m-30) cc_final: 0.7395 (m-30) REVERT: B 814 MET cc_start: 0.9008 (mmp) cc_final: 0.8747 (mmm) REVERT: B 828 GLU cc_start: 0.8758 (mp0) cc_final: 0.8540 (mp0) REVERT: C 513 ASN cc_start: 0.8282 (m-40) cc_final: 0.7343 (p0) REVERT: C 630 MET cc_start: 0.7857 (mpp) cc_final: 0.7547 (mpp) REVERT: C 675 ARG cc_start: 0.4731 (mtt180) cc_final: 0.4116 (mtt180) REVERT: C 688 ILE cc_start: 0.9285 (mm) cc_final: 0.9031 (tp) REVERT: C 750 ASP cc_start: 0.7058 (p0) cc_final: 0.5828 (t70) REVERT: C 751 GLU cc_start: 0.8187 (pt0) cc_final: 0.7468 (pm20) REVERT: C 754 TYR cc_start: 0.7934 (m-10) cc_final: 0.7400 (m-80) REVERT: C 773 GLU cc_start: 0.8380 (mp0) cc_final: 0.7906 (mp0) REVERT: C 779 VAL cc_start: 0.9274 (t) cc_final: 0.8999 (t) REVERT: C 819 LEU cc_start: 0.9259 (mt) cc_final: 0.9002 (pp) REVERT: D 570 ASP cc_start: 0.7650 (m-30) cc_final: 0.7294 (m-30) REVERT: D 608 PHE cc_start: 0.5994 (t80) cc_final: 0.5422 (t80) REVERT: D 610 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7863 (tptp) REVERT: D 612 PHE cc_start: 0.7727 (m-10) cc_final: 0.7155 (m-80) REVERT: D 676 PHE cc_start: 0.8592 (t80) cc_final: 0.8126 (t80) REVERT: D 681 TRP cc_start: 0.8728 (t60) cc_final: 0.8519 (t60) REVERT: D 722 ILE cc_start: 0.8863 (mt) cc_final: 0.8633 (mp) REVERT: D 754 TYR cc_start: 0.9117 (m-10) cc_final: 0.8660 (m-80) REVERT: D 772 ASP cc_start: 0.7868 (m-30) cc_final: 0.7525 (m-30) REVERT: D 828 GLU cc_start: 0.8709 (mp0) cc_final: 0.8495 (mp0) REVERT: D 837 TYR cc_start: 0.6087 (m-10) cc_final: 0.5756 (m-80) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.0910 time to fit residues: 49.5360 Evaluate side-chains 251 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 8.9990 chunk 138 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 5 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS ** 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 585 GLN D 725 GLN ** D 805 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 = 0.3608 r_free = 0.3608 target = 0.088851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071003 restraints weight = 50882.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073236 restraints weight = 32541.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.074856 restraints weight = 23662.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076014 restraints weight = 18657.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.076927 restraints weight = 15494.490| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12072 Z= 0.152 Angle : 0.693 13.021 16456 Z= 0.353 Chirality : 0.049 0.567 1898 Planarity : 0.005 0.050 2072 Dihedral : 5.480 24.860 1598 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % 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: -2.36 (0.20), residues: 1452 helix: -1.08 (0.17), residues: 732 sheet: -2.11 (0.37), residues: 178 loop : -1.83 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 832 TYR 0.012 0.001 TYR C 504 PHE 0.021 0.002 PHE D 626 TRP 0.014 0.001 TRP B 485 HIS 0.004 0.001 HIS C 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12060) covalent geometry : angle 0.66702 / 0.35 (16424) SS BOND : bond 0.00672 / 0.34 ( 4) SS BOND : angle 1.67707 / 1.03 ( 8) hydrogen bonds : bond 0.04614 / 3.02 ( 482) hydrogen bonds : angle 5.14748 / 3.68 ( 1464) link_BETA1-4 : bond 0.01038 / 0.53 ( 4) link_BETA1-4 : angle 2.80533 / 1.27 ( 12) link_NAG-ASN : bond 0.01864 / 0.96 ( 4) link_NAG-ASN : angle 6.32020 / 4.57 ( 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 321 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.281 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 681 TRP cc_start: 0.8782 (t60) cc_final: 0.8575 (t60) REVERT: A 749 LYS cc_start: 0.7586 (ptmt) cc_final: 0.7322 (ptpt) REVERT: A 754 TYR cc_start: 0.8462 (m-10) cc_final: 0.8012 (m-80) REVERT: A 772 ASP cc_start: 0.8698 (m-30) cc_final: 0.8470 (t70) REVERT: B 599 LYS cc_start: 0.6724 (ptpp) cc_final: 0.6405 (mmmt) REVERT: B 610 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8237 (tptp) REVERT: B 612 PHE cc_start: 0.7756 (m-80) cc_final: 0.7373 (m-80) REVERT: B 624 PHE cc_start: 0.7523 (t80) cc_final: 0.7315 (t80) REVERT: B 692 TYR cc_start: 0.8682 (t80) cc_final: 0.8447 (t80) REVERT: B 700 LEU cc_start: 0.9098 (mm) cc_final: 0.8732 (mm) REVERT: B 725 GLN cc_start: 0.7183 (tt0) cc_final: 0.6918 (tt0) REVERT: B 772 ASP cc_start: 0.7864 (m-30) cc_final: 0.7438 (m-30) REVERT: B 823 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 828 GLU cc_start: 0.8731 (mp0) cc_final: 0.8505 (mp0) REVERT: C 513 ASN cc_start: 0.8409 (m-40) cc_final: 0.7515 (p0) REVERT: C 630 MET cc_start: 0.7887 (mpp) cc_final: 0.7361 (mpp) REVERT: C 675 ARG cc_start: 0.4841 (mtt180) cc_final: 0.4248 (mtt180) REVERT: C 681 TRP cc_start: 0.8181 (t60) cc_final: 0.7892 (t60) REVERT: C 688 ILE cc_start: 0.9312 (mm) cc_final: 0.9063 (tp) REVERT: C 709 ILE cc_start: 0.7966 (mm) cc_final: 0.7503 (mm) REVERT: C 751 GLU cc_start: 0.8301 (pt0) cc_final: 0.7757 (pm20) REVERT: C 754 TYR cc_start: 0.7974 (m-10) cc_final: 0.7461 (m-80) REVERT: D 570 ASP cc_start: 0.7559 (m-30) cc_final: 0.7254 (m-30) REVERT: D 608 PHE cc_start: 0.5580 (t80) cc_final: 0.5059 (t80) REVERT: D 610 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7792 (tptp) REVERT: D 676 PHE cc_start: 0.8665 (t80) cc_final: 0.8196 (t80) REVERT: D 683 PHE cc_start: 0.8845 (t80) cc_final: 0.8644 (t80) REVERT: D 722 ILE cc_start: 0.8961 (mt) cc_final: 0.8725 (mp) REVERT: D 772 ASP cc_start: 0.7790 (m-30) cc_final: 0.7534 (m-30) REVERT: D 814 MET cc_start: 0.8629 (mmp) cc_final: 0.8393 (mmm) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.0768 time to fit residues: 37.6923 Evaluate side-chains 227 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 0.6980 chunk 142 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 805 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 = 0.3606 r_free = 0.3606 target = 0.088691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070617 restraints weight = 50407.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072868 restraints weight = 32126.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074449 restraints weight = 23320.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.075572 restraints weight = 18426.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.076477 restraints weight = 15398.073| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12072 Z= 0.135 Angle : 0.655 12.868 16456 Z= 0.334 Chirality : 0.047 0.301 1898 Planarity : 0.004 0.049 2072 Dihedral : 5.245 25.417 1598 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -1.67 (0.21), residues: 1452 helix: -0.40 (0.18), residues: 724 sheet: -1.85 (0.38), residues: 188 loop : -1.63 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 797 TYR 0.018 0.001 TYR C 552 PHE 0.024 0.001 PHE A 626 TRP 0.015 0.001 TRP D 681 HIS 0.004 0.001 HIS C 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12060) covalent geometry : angle 0.63377 / 0.33 (16424) SS BOND : bond 0.00203 / 0.10 ( 4) SS BOND : angle 1.45727 / 0.89 ( 8) hydrogen bonds : bond 0.03988 / 2.60 ( 482) hydrogen bonds : angle 4.86900 / 3.46 ( 1464) link_BETA1-4 : bond 0.01071 / 0.54 ( 4) link_BETA1-4 : angle 1.44581 / 0.80 ( 12) link_NAG-ASN : bond 0.01644 / 0.84 ( 4) link_NAG-ASN : angle 5.87842 / 3.89 ( 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 307 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.449 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 518 ARG cc_start: 0.8302 (tmt170) cc_final: 0.8080 (tpt90) REVERT: A 681 TRP cc_start: 0.8772 (t60) cc_final: 0.8529 (t60) REVERT: A 749 LYS cc_start: 0.7687 (ptmt) cc_final: 0.7241 (ptpt) REVERT: A 754 TYR cc_start: 0.8469 (m-10) cc_final: 0.7938 (m-80) REVERT: A 772 ASP cc_start: 0.8720 (m-30) cc_final: 0.8464 (t70) REVERT: A 793 GLN cc_start: 0.5658 (tp40) cc_final: 0.5118 (tp40) REVERT: B 599 LYS cc_start: 0.6940 (ptpp) cc_final: 0.6489 (mtpt) REVERT: B 610 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8176 (tptp) REVERT: B 700 LEU cc_start: 0.9104 (mm) cc_final: 0.8757 (mm) REVERT: B 828 GLU cc_start: 0.8732 (mp0) cc_final: 0.8499 (mp0) REVERT: C 513 ASN cc_start: 0.8515 (m-40) cc_final: 0.7578 (p0) REVERT: C 630 MET cc_start: 0.7928 (mpp) cc_final: 0.7477 (mpp) REVERT: C 675 ARG cc_start: 0.4725 (mtt180) cc_final: 0.4097 (mtt180) REVERT: C 681 TRP cc_start: 0.8250 (t60) cc_final: 0.7921 (t60) REVERT: C 709 ILE cc_start: 0.8033 (mm) cc_final: 0.7543 (mm) REVERT: C 754 TYR cc_start: 0.8067 (m-10) cc_final: 0.7634 (m-10) REVERT: C 779 VAL cc_start: 0.9221 (t) cc_final: 0.9019 (t) REVERT: C 843 MET cc_start: 0.5770 (tmm) cc_final: 0.5437 (tmm) REVERT: D 570 ASP cc_start: 0.7580 (m-30) cc_final: 0.7296 (m-30) REVERT: D 608 PHE cc_start: 0.5502 (t80) cc_final: 0.4952 (t80) REVERT: D 610 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7739 (tptp) REVERT: D 676 PHE cc_start: 0.8677 (t80) cc_final: 0.8455 (t80) REVERT: D 681 TRP cc_start: 0.8680 (t60) cc_final: 0.8466 (t60) REVERT: D 754 TYR cc_start: 0.8762 (m-80) cc_final: 0.8490 (m-80) REVERT: D 772 ASP cc_start: 0.7801 (m-30) cc_final: 0.7411 (m-30) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.0820 time to fit residues: 38.4060 Evaluate side-chains 219 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 0.9990 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.087826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069767 restraints weight = 50951.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071958 restraints weight = 32968.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073519 restraints weight = 24147.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074663 restraints weight = 19168.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075533 restraints weight = 16024.137| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12072 Z= 0.145 Angle : 0.654 12.907 16456 Z= 0.335 Chirality : 0.049 0.671 1898 Planarity : 0.004 0.047 2072 Dihedral : 5.162 25.317 1598 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -1.35 (0.22), residues: 1452 helix: -0.09 (0.19), residues: 728 sheet: -1.71 (0.39), residues: 182 loop : -1.56 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 495 TYR 0.020 0.002 TYR B 692 PHE 0.025 0.002 PHE D 683 TRP 0.011 0.001 TRP D 681 HIS 0.015 0.002 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12060) covalent geometry : angle 0.62919 / 0.33 (16424) SS BOND : bond 0.00176 / 0.09 ( 4) SS BOND : angle 1.88045 / 1.60 ( 8) hydrogen bonds : bond 0.03785 / 2.45 ( 482) hydrogen bonds : angle 4.76985 / 3.40 ( 1464) link_BETA1-4 : bond 0.00520 / 0.26 ( 4) link_BETA1-4 : angle 1.99330 / 0.90 ( 12) link_NAG-ASN : bond 0.01788 / 0.92 ( 4) link_NAG-ASN : angle 6.22796 / 4.52 ( 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 291 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.418 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: 0.9164 (mm) cc_final: 0.8953 (mm) REVERT: A 681 TRP cc_start: 0.8678 (t60) cc_final: 0.8468 (t60) REVERT: A 749 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7525 (ptpt) REVERT: A 754 TYR cc_start: 0.8459 (m-10) cc_final: 0.7921 (m-80) REVERT: A 772 ASP cc_start: 0.8638 (m-30) cc_final: 0.8403 (t70) REVERT: B 599 LYS cc_start: 0.7093 (ptpp) cc_final: 0.6673 (mmmt) REVERT: B 612 PHE cc_start: 0.7420 (m-80) cc_final: 0.7029 (m-80) REVERT: B 617 TRP cc_start: 0.7120 (m100) cc_final: 0.4815 (t-100) REVERT: B 700 LEU cc_start: 0.9129 (mm) cc_final: 0.8824 (mm) REVERT: B 772 ASP cc_start: 0.7866 (m-30) cc_final: 0.7310 (m-30) REVERT: B 828 GLU cc_start: 0.8715 (mp0) cc_final: 0.8514 (mp0) REVERT: C 620 THR cc_start: 0.8408 (m) cc_final: 0.8203 (p) REVERT: C 630 MET cc_start: 0.7997 (mpp) cc_final: 0.7405 (mpp) REVERT: C 675 ARG cc_start: 0.4729 (mtt180) cc_final: 0.4192 (mtt180) REVERT: C 681 TRP cc_start: 0.8271 (t60) cc_final: 0.8006 (t60) REVERT: C 691 SER cc_start: 0.9053 (m) cc_final: 0.8745 (p) REVERT: C 709 ILE cc_start: 0.8121 (mm) cc_final: 0.7637 (mm) REVERT: C 754 TYR cc_start: 0.7779 (m-10) cc_final: 0.7502 (m-80) REVERT: D 608 PHE cc_start: 0.5424 (t80) cc_final: 0.4971 (t80) REVERT: D 610 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7772 (tptp) REVERT: D 676 PHE cc_start: 0.8621 (t80) cc_final: 0.8363 (t80) REVERT: D 814 MET cc_start: 0.8765 (mmp) cc_final: 0.8547 (mmp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.0789 time to fit residues: 35.2223 Evaluate side-chains 227 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 704 GLN B 704 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 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 704 GLN D 725 GLN ** D 805 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 = 0.3531 r_free = 0.3531 target = 0.084523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066933 restraints weight = 52396.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069102 restraints weight = 33078.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070616 restraints weight = 23960.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071737 restraints weight = 18951.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072540 restraints weight = 15829.982| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12072 Z= 0.213 Angle : 0.737 13.549 16456 Z= 0.380 Chirality : 0.049 0.392 1898 Planarity : 0.005 0.044 2072 Dihedral : 5.458 26.694 1598 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % 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: -1.43 (0.22), residues: 1452 helix: -0.04 (0.18), residues: 738 sheet: -1.76 (0.39), residues: 182 loop : -1.82 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 501 TYR 0.022 0.002 TYR C 552 PHE 0.022 0.002 PHE A 623 TRP 0.019 0.002 TRP A 859 HIS 0.008 0.001 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (12060) covalent geometry : angle 0.71515 / 0.38 (16424) SS BOND : bond 0.00773 / 0.38 ( 4) SS BOND : angle 1.94424 / 1.35 ( 8) hydrogen bonds : bond 0.03980 / 2.60 ( 482) hydrogen bonds : angle 4.87879 / 3.45 ( 1464) link_BETA1-4 : bond 0.00943 / 0.48 ( 4) link_BETA1-4 : angle 1.42807 / 0.93 ( 12) link_NAG-ASN : bond 0.01657 / 0.85 ( 4) link_NAG-ASN : angle 6.37130 / 4.25 ( 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 271 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 TYR cc_start: 0.7622 (m-80) cc_final: 0.7370 (m-80) REVERT: A 570 ASP cc_start: 0.8237 (m-30) cc_final: 0.7890 (m-30) REVERT: A 626 PHE cc_start: 0.7727 (t80) cc_final: 0.7366 (t80) REVERT: A 675 ARG cc_start: 0.5995 (mtt180) cc_final: 0.5681 (mtt180) REVERT: A 681 TRP cc_start: 0.8648 (t60) cc_final: 0.8443 (t60) REVERT: A 749 LYS cc_start: 0.7985 (ptmt) cc_final: 0.7662 (ptpt) REVERT: A 754 TYR cc_start: 0.8472 (m-10) cc_final: 0.7943 (m-80) REVERT: A 855 LEU cc_start: 0.7683 (mm) cc_final: 0.7373 (tp) REVERT: B 599 LYS cc_start: 0.7260 (ptpp) cc_final: 0.6557 (mmmt) REVERT: B 610 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8412 (tptp) REVERT: B 617 TRP cc_start: 0.7248 (m100) cc_final: 0.5025 (t-100) REVERT: B 681 TRP cc_start: 0.7934 (t60) cc_final: 0.7624 (t60) REVERT: B 689 ASN cc_start: 0.9100 (t0) cc_final: 0.8896 (t0) REVERT: B 700 LEU cc_start: 0.9241 (mm) cc_final: 0.8966 (mm) REVERT: B 828 GLU cc_start: 0.8731 (mp0) cc_final: 0.8520 (mp0) REVERT: C 562 ASP cc_start: 0.8711 (t70) cc_final: 0.8427 (t0) REVERT: C 592 LEU cc_start: 0.9326 (mt) cc_final: 0.9039 (mt) REVERT: C 630 MET cc_start: 0.8117 (mpp) cc_final: 0.7500 (mpp) REVERT: C 632 TRP cc_start: 0.6774 (t60) cc_final: 0.6528 (t60) REVERT: C 675 ARG cc_start: 0.5158 (mtt180) cc_final: 0.4878 (mtt180) REVERT: C 681 TRP cc_start: 0.8300 (t60) cc_final: 0.7862 (t60) REVERT: C 695 SER cc_start: 0.8987 (m) cc_final: 0.8666 (t) REVERT: C 709 ILE cc_start: 0.8010 (mm) cc_final: 0.7617 (mm) REVERT: C 814 MET cc_start: 0.9227 (mmp) cc_final: 0.9017 (mmp) REVERT: D 610 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7881 (tptp) REVERT: D 612 PHE cc_start: 0.7357 (m-80) cc_final: 0.6997 (m-10) REVERT: D 879 ARG cc_start: 0.6840 (tpt-90) cc_final: 0.6338 (mmt90) REVERT: A 1001 GLU cc_start: 0.7094 (tt0) cc_final: 0.6350 (tt0) outliers start: 1 outliers final: 1 residues processed: 271 average time/residue: 0.0836 time to fit residues: 34.1948 Evaluate side-chains 212 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 0.9990 chunk 90 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 704 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 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 = 0.3526 r_free = 0.3526 target = 0.084520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066963 restraints weight = 52069.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069119 restraints weight = 33103.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070594 restraints weight = 24083.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071693 restraints weight = 19140.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072412 restraints weight = 16110.578| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12072 Z= 0.191 Angle : 0.728 13.594 16456 Z= 0.367 Chirality : 0.052 0.881 1898 Planarity : 0.005 0.044 2072 Dihedral : 5.428 23.837 1598 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -1.26 (0.22), residues: 1452 helix: 0.13 (0.19), residues: 734 sheet: -1.80 (0.40), residues: 182 loop : -1.74 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 806 TYR 0.017 0.002 TYR C 552 PHE 0.019 0.002 PHE C 564 TRP 0.017 0.002 TRP D 632 HIS 0.003 0.001 HIS B 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (12060) covalent geometry : angle 0.69902 / 0.36 (16424) SS BOND : bond 0.00890 / 0.45 ( 4) SS BOND : angle 2.09987 / 1.23 ( 8) hydrogen bonds : bond 0.03813 / 2.46 ( 482) hydrogen bonds : angle 4.86653 / 3.44 ( 1464) link_BETA1-4 : bond 0.00876 / 0.44 ( 4) link_BETA1-4 : angle 1.99916 / 0.91 ( 12) link_NAG-ASN : bond 0.01571 / 0.80 ( 4) link_NAG-ASN : angle 7.09554 / 5.50 ( 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 263 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.379 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 570 ASP cc_start: 0.8136 (m-30) cc_final: 0.7599 (m-30) REVERT: A 626 PHE cc_start: 0.7681 (t80) cc_final: 0.7343 (t80) REVERT: A 675 ARG cc_start: 0.6108 (mtt180) cc_final: 0.5784 (mtt180) REVERT: A 749 LYS cc_start: 0.7982 (ptmt) cc_final: 0.7645 (ptpt) REVERT: A 751 GLU cc_start: 0.8372 (pm20) cc_final: 0.8012 (pm20) REVERT: A 754 TYR cc_start: 0.8482 (m-10) cc_final: 0.7937 (m-80) REVERT: A 789 ARG cc_start: 0.7799 (tpt90) cc_final: 0.7532 (tpp-160) REVERT: A 855 LEU cc_start: 0.7499 (mm) cc_final: 0.7296 (tp) REVERT: B 599 LYS cc_start: 0.7421 (ptpp) cc_final: 0.6621 (mmtt) REVERT: B 610 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8396 (tptp) REVERT: B 617 TRP cc_start: 0.7332 (m100) cc_final: 0.5238 (t-100) REVERT: B 630 MET cc_start: 0.7520 (ppp) cc_final: 0.7060 (ppp) REVERT: B 828 GLU cc_start: 0.8740 (mp0) cc_final: 0.8519 (mp0) REVERT: C 562 ASP cc_start: 0.8685 (t70) cc_final: 0.8411 (t0) REVERT: C 630 MET cc_start: 0.8198 (mpp) cc_final: 0.7605 (mpp) REVERT: C 675 ARG cc_start: 0.5499 (mtt180) cc_final: 0.5176 (mtt180) REVERT: C 695 SER cc_start: 0.8989 (m) cc_final: 0.8700 (t) REVERT: C 709 ILE cc_start: 0.8126 (mm) cc_final: 0.7856 (mm) REVERT: D 610 LYS cc_start: 0.8447 (ttpt) cc_final: 0.7937 (tptp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.0863 time to fit residues: 33.7296 Evaluate side-chains 205 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 0.7980 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 704 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.086097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068274 restraints weight = 51269.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070483 restraints weight = 32419.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.072024 restraints weight = 23534.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073153 restraints weight = 18653.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073945 restraints weight = 15646.732| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12072 Z= 0.137 Angle : 0.672 13.003 16456 Z= 0.338 Chirality : 0.048 0.585 1898 Planarity : 0.004 0.045 2072 Dihedral : 5.235 28.908 1598 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.08 % Allowed : 1.11 % Favored : 98.81 % 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: -1.03 (0.22), residues: 1452 helix: 0.40 (0.19), residues: 730 sheet: -1.79 (0.39), residues: 182 loop : -1.69 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 518 TYR 0.015 0.001 TYR C 552 PHE 0.037 0.002 PHE C 564 TRP 0.023 0.001 TRP D 617 HIS 0.002 0.000 HIS C 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12060) covalent geometry : angle 0.64879 / 0.33 (16424) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 1.88961 / 1.10 ( 8) hydrogen bonds : bond 0.03478 / 2.25 ( 482) hydrogen bonds : angle 4.65213 / 3.31 ( 1464) link_BETA1-4 : bond 0.00888 / 0.45 ( 4) link_BETA1-4 : angle 1.38868 / 0.73 ( 12) link_NAG-ASN : bond 0.01725 / 0.89 ( 4) link_NAG-ASN : angle 6.18429 / 4.45 ( 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 267 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 TYR cc_start: 0.7524 (m-80) cc_final: 0.7304 (m-80) REVERT: A 626 PHE cc_start: 0.7679 (t80) cc_final: 0.7196 (m-80) REVERT: A 675 ARG cc_start: 0.6019 (mtt180) cc_final: 0.5704 (mtt180) REVERT: A 681 TRP cc_start: 0.8664 (t60) cc_final: 0.8276 (t60) REVERT: A 722 ILE cc_start: 0.8642 (mt) cc_final: 0.8425 (tt) REVERT: A 749 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7599 (ptpt) REVERT: A 751 GLU cc_start: 0.8381 (pm20) cc_final: 0.8028 (pm20) REVERT: A 754 TYR cc_start: 0.8492 (m-10) cc_final: 0.7963 (m-80) REVERT: A 855 LEU cc_start: 0.7451 (mm) cc_final: 0.7208 (tp) REVERT: B 570 ASP cc_start: 0.6977 (m-30) cc_final: 0.6643 (m-30) REVERT: B 599 LYS cc_start: 0.7469 (ptpp) cc_final: 0.6603 (mmtt) REVERT: B 610 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8371 (tptp) REVERT: B 630 MET cc_start: 0.7578 (ppp) cc_final: 0.7211 (ppp) REVERT: B 700 LEU cc_start: 0.9149 (mm) cc_final: 0.8900 (mm) REVERT: B 828 GLU cc_start: 0.8767 (mp0) cc_final: 0.8541 (mp0) REVERT: C 630 MET cc_start: 0.8219 (mpp) cc_final: 0.7594 (mpp) REVERT: C 675 ARG cc_start: 0.5780 (mtt180) cc_final: 0.5485 (mtt180) REVERT: C 695 SER cc_start: 0.8918 (m) cc_final: 0.8655 (t) REVERT: C 709 ILE cc_start: 0.8184 (mm) cc_final: 0.7937 (mm) REVERT: C 814 MET cc_start: 0.9237 (mmp) cc_final: 0.9033 (mmp) REVERT: D 494 LEU cc_start: 0.8946 (tp) cc_final: 0.8639 (tt) REVERT: D 610 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7871 (tptp) REVERT: A 1001 GLU cc_start: 0.6934 (tt0) cc_final: 0.6387 (tt0) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.0910 time to fit residues: 36.5544 Evaluate side-chains 204 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 704 GLN A 725 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068638 restraints weight = 50939.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070880 restraints weight = 31993.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072438 restraints weight = 23133.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073605 restraints weight = 18297.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.074430 restraints weight = 15285.423| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12072 Z= 0.137 Angle : 0.667 12.701 16456 Z= 0.337 Chirality : 0.048 0.487 1898 Planarity : 0.004 0.045 2072 Dihedral : 5.178 24.231 1598 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.21 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: -0.95 (0.22), residues: 1452 helix: 0.48 (0.19), residues: 730 sheet: -1.69 (0.38), residues: 192 loop : -1.70 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 518 TYR 0.012 0.001 TYR C 552 PHE 0.022 0.001 PHE D 626 TRP 0.036 0.002 TRP D 617 HIS 0.011 0.002 HIS A 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12060) covalent geometry : angle 0.64671 / 0.33 (16424) SS BOND : bond 0.00177 / 0.09 ( 4) SS BOND : angle 1.52674 / 0.93 ( 8) hydrogen bonds : bond 0.03437 / 2.23 ( 482) hydrogen bonds : angle 4.63652 / 3.29 ( 1464) link_BETA1-4 : bond 0.00831 / 0.42 ( 4) link_BETA1-4 : angle 1.25825 / 0.69 ( 12) link_NAG-ASN : bond 0.01660 / 0.86 ( 4) link_NAG-ASN : angle 5.93148 / 4.15 ( 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 259 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7532 (m-80) cc_final: 0.6907 (m-80) REVERT: A 626 PHE cc_start: 0.7665 (t80) cc_final: 0.7438 (m-80) REVERT: A 680 ILE cc_start: 0.9229 (mm) cc_final: 0.9028 (mm) REVERT: A 722 ILE cc_start: 0.8671 (mt) cc_final: 0.8394 (tt) REVERT: A 749 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7588 (ptpt) REVERT: A 751 GLU cc_start: 0.8439 (pm20) cc_final: 0.8092 (pm20) REVERT: A 754 TYR cc_start: 0.8487 (m-10) cc_final: 0.7960 (m-80) REVERT: B 570 ASP cc_start: 0.7077 (m-30) cc_final: 0.6622 (m-30) REVERT: B 610 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8354 (tptp) REVERT: B 630 MET cc_start: 0.7554 (ppp) cc_final: 0.7220 (ppp) REVERT: B 681 TRP cc_start: 0.7926 (t60) cc_final: 0.7240 (t-100) REVERT: B 828 GLU cc_start: 0.8762 (mp0) cc_final: 0.8537 (mp0) REVERT: C 630 MET cc_start: 0.8226 (mpp) cc_final: 0.7606 (mpp) REVERT: C 675 ARG cc_start: 0.5739 (mtt180) cc_final: 0.5337 (mtt180) REVERT: C 695 SER cc_start: 0.8920 (m) cc_final: 0.8685 (t) REVERT: C 814 MET cc_start: 0.9236 (mmp) cc_final: 0.9024 (mmp) REVERT: D 494 LEU cc_start: 0.8937 (tp) cc_final: 0.8645 (tt) REVERT: D 610 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7850 (tptp) REVERT: D 814 MET cc_start: 0.8912 (mmp) cc_final: 0.8697 (mmm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.0921 time to fit residues: 35.7794 Evaluate side-chains 204 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 125 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 704 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3571 r_free = 0.3571 target = 0.086918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069029 restraints weight = 51566.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071309 restraints weight = 32325.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072888 restraints weight = 23306.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.074054 restraints weight = 18388.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.074847 restraints weight = 15401.960| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12072 Z= 0.132 Angle : 0.666 12.413 16456 Z= 0.336 Chirality : 0.048 0.450 1898 Planarity : 0.004 0.044 2072 Dihedral : 5.077 24.024 1598 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -0.88 (0.22), residues: 1452 helix: 0.57 (0.19), residues: 720 sheet: -1.35 (0.40), residues: 174 loop : -1.83 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 797 TYR 0.023 0.001 TYR C 754 PHE 0.022 0.001 PHE B 858 TRP 0.030 0.001 TRP A 681 HIS 0.002 0.001 HIS B 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12060) covalent geometry : angle 0.64711 / 0.33 (16424) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 1.48017 / 0.90 ( 8) hydrogen bonds : bond 0.03430 / 2.22 ( 482) hydrogen bonds : angle 4.58166 / 3.26 ( 1464) link_BETA1-4 : bond 0.00846 / 0.43 ( 4) link_BETA1-4 : angle 1.24158 / 0.68 ( 12) link_NAG-ASN : bond 0.01566 / 0.81 ( 4) link_NAG-ASN : angle 5.73242 / 3.98 ( 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 258 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7396 (m-80) cc_final: 0.6938 (m-80) REVERT: A 570 ASP cc_start: 0.7994 (m-30) cc_final: 0.7156 (m-30) REVERT: A 626 PHE cc_start: 0.7677 (t80) cc_final: 0.7073 (t80) REVERT: A 722 ILE cc_start: 0.8675 (mt) cc_final: 0.8405 (tt) REVERT: A 749 LYS cc_start: 0.7811 (ptmt) cc_final: 0.7460 (ptpt) REVERT: A 751 GLU cc_start: 0.8360 (pm20) cc_final: 0.7932 (pm20) REVERT: A 754 TYR cc_start: 0.8360 (m-10) cc_final: 0.7822 (m-80) REVERT: B 570 ASP cc_start: 0.7022 (m-30) cc_final: 0.6708 (m-30) REVERT: B 610 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8559 (mtpp) REVERT: B 681 TRP cc_start: 0.7938 (t60) cc_final: 0.7320 (t-100) REVERT: B 814 MET cc_start: 0.8717 (mmp) cc_final: 0.8488 (mmm) REVERT: B 828 GLU cc_start: 0.8720 (mp0) cc_final: 0.8483 (mp0) REVERT: C 630 MET cc_start: 0.8235 (mpp) cc_final: 0.7571 (mpp) REVERT: C 675 ARG cc_start: 0.5842 (mtt180) cc_final: 0.5360 (mtt180) REVERT: C 695 SER cc_start: 0.8936 (m) cc_final: 0.8701 (t) REVERT: D 494 LEU cc_start: 0.8977 (tp) cc_final: 0.8668 (tt) REVERT: D 496 ILE cc_start: 0.8140 (mp) cc_final: 0.7936 (mp) REVERT: D 610 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7847 (tptp) REVERT: D 700 LEU cc_start: 0.9467 (mm) cc_final: 0.9201 (mm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.0847 time to fit residues: 33.3130 Evaluate side-chains 209 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.086952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069054 restraints weight = 52847.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071218 restraints weight = 33449.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072765 restraints weight = 24453.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073820 restraints weight = 19454.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074612 restraints weight = 16530.630| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12072 Z= 0.136 Angle : 0.656 12.236 16456 Z= 0.331 Chirality : 0.048 0.440 1898 Planarity : 0.004 0.045 2072 Dihedral : 4.997 24.392 1598 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.08 % Allowed : 0.56 % Favored : 99.37 % 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: -0.87 (0.22), residues: 1452 helix: 0.60 (0.19), residues: 720 sheet: -1.59 (0.38), residues: 192 loop : -1.73 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 518 TYR 0.012 0.001 TYR C 552 PHE 0.029 0.001 PHE B 612 TRP 0.014 0.001 TRP D 681 HIS 0.002 0.000 HIS C 831 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12060) covalent geometry : angle 0.63695 / 0.33 (16424) SS BOND : bond 0.00159 / 0.08 ( 4) SS BOND : angle 1.43338 / 0.88 ( 8) hydrogen bonds : bond 0.03366 / 2.15 ( 482) hydrogen bonds : angle 4.58089 / 3.24 ( 1464) link_BETA1-4 : bond 0.00760 / 0.39 ( 4) link_BETA1-4 : angle 1.19669 / 0.66 ( 12) link_NAG-ASN : bond 0.01543 / 0.79 ( 4) link_NAG-ASN : angle 5.61074 / 3.88 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.08 seconds wall clock time: 32 minutes 16.15 seconds (1936.15 seconds total)