Starting phenix.real_space_refine on Wed Jul 30 04:34:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lzi_23607/07_2025/7lzi_23607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lzi_23607/07_2025/7lzi_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_2025/7lzi_23607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2025/7lzi_23607.map" model { file = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2025/7lzi_23607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lzi_23607/07_2025/7lzi_23607.cif" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11782 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2946 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2869 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2946 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2869 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 7.67, per 1000 atoms: 0.65 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.54 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: 3.43 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3706 1.34 - 1.46: 2886 1.46 - 1.58: 5412 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 12060 Sorted by residual: bond pdb=" C LEU B 774 " pdb=" N PRO B 775 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.06e-02 8.90e+03 1.40e+01 bond pdb=" C LEU D 774 " pdb=" N PRO D 775 " ideal model delta sigma weight residual 1.337 1.376 -0.039 1.06e-02 8.90e+03 1.38e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" N ASN D 719 " pdb=" CA ASN D 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.06e+00 ... (remaining 12055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 16125 2.76 - 5.51: 250 5.51 - 8.27: 43 8.27 - 11.02: 4 11.02 - 13.78: 2 Bond angle restraints: 16424 Sorted by residual: angle pdb=" C SER C 718 " pdb=" N ASN C 719 " pdb=" CA ASN C 719 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C SER A 718 " pdb=" N ASN A 719 " pdb=" CA ASN A 719 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C SER D 603 " pdb=" N SER D 604 " pdb=" CA SER D 604 " ideal model delta sigma weight residual 122.29 128.43 -6.14 1.48e+00 4.57e-01 1.72e+01 angle pdb=" C SER B 603 " pdb=" N SER B 604 " pdb=" CA SER B 604 " ideal model delta sigma weight residual 122.29 128.39 -6.10 1.48e+00 4.57e-01 1.70e+01 angle pdb=" CA LEU B 609 " pdb=" CB LEU B 609 " pdb=" CG LEU B 609 " ideal model delta sigma weight residual 116.30 130.08 -13.78 3.50e+00 8.16e-02 1.55e+01 ... (remaining 16419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 6857 20.55 - 41.10: 271 41.10 - 61.65: 40 61.65 - 82.20: 12 82.20 - 102.75: 16 Dihedral angle restraints: 7196 sinusoidal: 2910 harmonic: 4286 Sorted by residual: dihedral pdb=" CA PHE A 623 " pdb=" C PHE A 623 " pdb=" N PHE A 624 " pdb=" CA PHE A 624 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE C 623 " pdb=" C PHE C 623 " pdb=" N PHE C 624 " pdb=" CA PHE C 624 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA THR B 613 " pdb=" C THR B 613 " pdb=" N ILE B 614 " pdb=" CA ILE B 614 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 1892 0.205 - 0.411: 4 0.411 - 0.616: 0 0.616 - 0.821: 1 0.821 - 1.027: 1 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 576 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 576 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" CA ASN A 719 " pdb=" N ASN A 719 " pdb=" C ASN A 719 " pdb=" CB ASN A 719 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1895 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 576 " 0.005 2.00e-02 2.50e+03 3.35e-02 1.40e+01 pdb=" CG ASN A 576 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 576 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 576 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 612 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C PHE B 612 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE B 612 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 613 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 612 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C PHE D 612 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE D 612 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 613 " 0.018 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2263 2.77 - 3.30: 11140 3.30 - 3.83: 19136 3.83 - 4.37: 22411 4.37 - 4.90: 36977 Nonbonded interactions: 91927 Sorted by model distance: nonbonded pdb=" OG1 THR A 613 " pdb=" O LYS D 856 " model vdw 2.234 3.040 nonbonded pdb=" O TRP B 485 " pdb=" OH TYR B 534 " model vdw 2.272 3.040 nonbonded pdb=" O TRP D 485 " pdb=" OH TYR D 534 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU B 526 " pdb=" OH TYR B 540 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU D 526 " pdb=" OH TYR D 540 " model vdw 2.300 3.040 ... (remaining 91922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 483 through 842 or resid 853 through 880 or resid 1001)) selection = chain 'B' selection = (chain 'C' and (resid 483 through 842 or resid 853 through 880 or resid 1001)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.820 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12072 Z= 0.248 Angle : 0.976 15.363 16456 Z= 0.533 Chirality : 0.063 1.027 1898 Planarity : 0.007 0.060 2072 Dihedral : 13.062 102.751 4416 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.32 % Allowed : 6.35 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP A 681 HIS 0.004 0.001 HIS D 831 PHE 0.018 0.002 PHE B 795 TYR 0.024 0.002 TYR C 552 ARG 0.008 0.001 ARG A 548 Details of bonding type rmsd link_NAG-ASN : bond 0.03804 ( 4) link_NAG-ASN : angle 8.57110 ( 12) link_BETA1-4 : bond 0.02179 ( 4) link_BETA1-4 : angle 4.47426 ( 12) hydrogen bonds : bond 0.29658 ( 482) hydrogen bonds : angle 9.39239 ( 1464) SS BOND : bond 0.00122 ( 4) SS BOND : angle 2.12299 ( 8) covalent geometry : bond 0.00484 (12060) covalent geometry : angle 0.94027 (16424) *********************** 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 : 1.302 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: 0.8724 (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: 0.7520 (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: 0.9068 (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: 0.9023 (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: 0.8699 (tppt) cc_final: 0.8347 (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: 0.2440 time to fit residues: 174.6715 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 : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS B 549 ASN B 554 ASN B 704 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 554 ASN C 563 ASN C 704 GLN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3598 r_free = 0.3598 target = 0.088667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070530 restraints weight = 50405.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072745 restraints weight = 32710.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074284 restraints weight = 23959.260| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12072 Z= 0.181 Angle : 0.741 12.234 16456 Z= 0.381 Chirality : 0.049 0.380 1898 Planarity : 0.006 0.051 2072 Dihedral : 10.507 79.060 1766 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.19), residues: 1452 helix: -1.89 (0.15), residues: 726 sheet: -2.43 (0.36), residues: 176 loop : -2.09 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 878 HIS 0.004 0.001 HIS A 831 PHE 0.026 0.002 PHE D 626 TYR 0.012 0.002 TYR A 552 ARG 0.012 0.001 ARG C 832 Details of bonding type rmsd link_NAG-ASN : bond 0.01502 ( 4) link_NAG-ASN : angle 6.31708 ( 12) link_BETA1-4 : bond 0.00979 ( 4) link_BETA1-4 : angle 3.07619 ( 12) hydrogen bonds : bond 0.05745 ( 482) hydrogen bonds : angle 5.65292 ( 1464) SS BOND : bond 0.00187 ( 4) SS BOND : angle 1.12952 ( 8) covalent geometry : bond 0.00387 (12060) covalent geometry : angle 0.71614 (16424) *********************** 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 361 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 PHE cc_start: 0.7510 (t80) cc_final: 0.6933 (t80) REVERT: A 680 ILE cc_start: 0.9197 (mm) cc_final: 0.8974 (mm) REVERT: A 695 SER cc_start: 0.9136 (m) cc_final: 0.8875 (t) REVERT: A 749 LYS cc_start: 0.7587 (ptmt) cc_final: 0.7166 (ptpt) REVERT: A 754 TYR cc_start: 0.8414 (m-10) cc_final: 0.7916 (m-80) REVERT: A 772 ASP cc_start: 0.8650 (m-30) cc_final: 0.8428 (t70) REVERT: A 829 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8570 (mmmm) REVERT: A 850 ASP cc_start: 0.5951 (t0) cc_final: 0.5701 (t0) REVERT: B 564 PHE cc_start: 0.8235 (m-80) cc_final: 0.7963 (m-10) REVERT: B 599 LYS cc_start: 0.6775 (ptpp) cc_final: 0.6392 (mmmt) REVERT: B 610 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8331 (tptp) REVERT: B 612 PHE cc_start: 0.7783 (m-80) cc_final: 0.7253 (m-80) REVERT: B 689 ASN cc_start: 0.8719 (t0) cc_final: 0.8445 (t0) REVERT: B 692 TYR cc_start: 0.8617 (t80) cc_final: 0.8272 (t80) REVERT: B 700 LEU cc_start: 0.9189 (mm) cc_final: 0.8795 (mm) REVERT: B 722 ILE cc_start: 0.8610 (mt) cc_final: 0.8394 (mp) REVERT: B 746 VAL cc_start: 0.9042 (t) cc_final: 0.8838 (m) REVERT: B 759 GLN cc_start: 0.8923 (mm110) cc_final: 0.8493 (mm-40) REVERT: B 767 VAL cc_start: 0.8674 (m) cc_final: 0.8435 (m) REVERT: B 772 ASP cc_start: 0.7885 (m-30) cc_final: 0.7434 (m-30) REVERT: B 814 MET cc_start: 0.9013 (mmp) cc_final: 0.8798 (mmm) REVERT: C 513 ASN cc_start: 0.8309 (m-40) cc_final: 0.7332 (p0) REVERT: C 630 MET cc_start: 0.7859 (mpp) cc_final: 0.7520 (mpp) REVERT: C 675 ARG cc_start: 0.4944 (mtt180) cc_final: 0.4349 (mtt180) REVERT: C 688 ILE cc_start: 0.9287 (mm) cc_final: 0.9034 (tp) REVERT: C 750 ASP cc_start: 0.7008 (p0) cc_final: 0.5833 (t70) REVERT: C 751 GLU cc_start: 0.8255 (pt0) cc_final: 0.7492 (pm20) REVERT: C 754 TYR cc_start: 0.7951 (m-10) cc_final: 0.7433 (m-80) REVERT: C 773 GLU cc_start: 0.8355 (mp0) cc_final: 0.7910 (mp0) REVERT: C 779 VAL cc_start: 0.9271 (t) cc_final: 0.8982 (p) REVERT: C 819 LEU cc_start: 0.9281 (mt) cc_final: 0.9012 (pp) REVERT: D 570 ASP cc_start: 0.7602 (m-30) cc_final: 0.7281 (m-30) REVERT: D 608 PHE cc_start: 0.6089 (t80) cc_final: 0.5490 (t80) REVERT: D 610 LYS cc_start: 0.8522 (ttpt) cc_final: 0.7983 (tptp) REVERT: D 612 PHE cc_start: 0.7749 (m-10) cc_final: 0.7276 (m-80) REVERT: D 676 PHE cc_start: 0.8587 (t80) cc_final: 0.8093 (t80) REVERT: D 722 ILE cc_start: 0.8819 (mt) cc_final: 0.8593 (mp) REVERT: D 754 TYR cc_start: 0.9106 (m-10) cc_final: 0.8672 (m-80) REVERT: D 772 ASP cc_start: 0.7848 (m-30) cc_final: 0.7515 (m-30) REVERT: D 828 GLU cc_start: 0.8732 (mp0) cc_final: 0.8514 (mp0) REVERT: D 837 TYR cc_start: 0.6257 (m-10) cc_final: 0.5795 (m-80) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.2226 time to fit residues: 115.1257 Evaluate side-chains 239 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 0.0070 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN D 704 GLN D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068114 restraints weight = 52218.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070275 restraints weight = 33469.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071787 restraints weight = 24412.952| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4702 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= 0.218 Angle : 0.793 16.309 16456 Z= 0.398 Chirality : 0.050 0.587 1898 Planarity : 0.005 0.051 2072 Dihedral : 8.809 57.935 1766 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1452 helix: -1.05 (0.17), residues: 732 sheet: -2.16 (0.39), residues: 172 loop : -2.01 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 485 HIS 0.003 0.001 HIS A 831 PHE 0.021 0.002 PHE D 626 TYR 0.022 0.002 TYR A 580 ARG 0.019 0.001 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01711 ( 4) link_NAG-ASN : angle 7.23984 ( 12) link_BETA1-4 : bond 0.00999 ( 4) link_BETA1-4 : angle 3.57946 ( 12) hydrogen bonds : bond 0.04790 ( 482) hydrogen bonds : angle 5.30968 ( 1464) SS BOND : bond 0.00142 ( 4) SS BOND : angle 1.28617 ( 8) covalent geometry : bond 0.00477 (12060) covalent geometry : angle 0.76308 (16424) *********************** 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 304 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 PHE cc_start: 0.7458 (t80) cc_final: 0.7195 (t80) REVERT: A 681 TRP cc_start: 0.8764 (t60) cc_final: 0.8546 (t60) REVERT: A 751 GLU cc_start: 0.8287 (pm20) cc_final: 0.8078 (pm20) REVERT: A 754 TYR cc_start: 0.8456 (m-10) cc_final: 0.8007 (m-80) REVERT: A 814 MET cc_start: 0.9039 (mtp) cc_final: 0.8818 (mtp) REVERT: A 850 ASP cc_start: 0.5895 (t0) cc_final: 0.5507 (t0) REVERT: B 599 LYS cc_start: 0.6978 (ptpp) cc_final: 0.6524 (mmmt) REVERT: B 610 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8241 (tptp) REVERT: B 689 ASN cc_start: 0.8862 (t0) cc_final: 0.8645 (t0) REVERT: B 700 LEU cc_start: 0.9247 (mm) cc_final: 0.8942 (mm) REVERT: B 746 VAL cc_start: 0.9082 (t) cc_final: 0.8874 (m) REVERT: B 759 GLN cc_start: 0.8903 (mm110) cc_final: 0.8472 (mm-40) REVERT: B 767 VAL cc_start: 0.8695 (m) cc_final: 0.8479 (m) REVERT: B 832 ARG cc_start: 0.8423 (mpp80) cc_final: 0.8097 (mtm110) REVERT: C 562 ASP cc_start: 0.8327 (t0) cc_final: 0.7944 (t70) REVERT: C 630 MET cc_start: 0.8040 (mpp) cc_final: 0.7410 (mpp) REVERT: C 675 ARG cc_start: 0.4847 (mtt180) cc_final: 0.4254 (mtt180) REVERT: C 681 TRP cc_start: 0.8317 (t60) cc_final: 0.7884 (t60) REVERT: C 750 ASP cc_start: 0.7258 (p0) cc_final: 0.6625 (t70) REVERT: C 751 GLU cc_start: 0.8461 (pt0) cc_final: 0.8063 (pm20) REVERT: C 843 MET cc_start: 0.6022 (tmm) cc_final: 0.5579 (tmm) REVERT: C 861 LEU cc_start: 0.8943 (tp) cc_final: 0.8704 (tp) REVERT: D 608 PHE cc_start: 0.5843 (t80) cc_final: 0.5481 (t80) REVERT: D 610 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8004 (tptp) REVERT: D 676 PHE cc_start: 0.8605 (t80) cc_final: 0.8364 (t80) REVERT: D 722 ILE cc_start: 0.8927 (mt) cc_final: 0.8712 (mp) REVERT: D 749 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8294 (mmtm) REVERT: D 772 ASP cc_start: 0.7733 (m-30) cc_final: 0.7399 (m-30) REVERT: D 814 MET cc_start: 0.8686 (mmp) cc_final: 0.8477 (mmm) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.2050 time to fit residues: 92.7406 Evaluate side-chains 215 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 70 optimal weight: 0.0470 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 736 ASN ** 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 = 0.3576 r_free = 0.3576 target = 0.086957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069141 restraints weight = 51139.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071246 restraints weight = 32889.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072751 restraints weight = 24167.039| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12072 Z= 0.147 Angle : 0.696 13.585 16456 Z= 0.350 Chirality : 0.049 0.688 1898 Planarity : 0.004 0.050 2072 Dihedral : 7.510 45.476 1766 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.24 % Allowed : 2.38 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1452 helix: -0.47 (0.18), residues: 732 sheet: -1.97 (0.40), residues: 172 loop : -1.76 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 681 HIS 0.015 0.002 HIS A 831 PHE 0.021 0.001 PHE D 626 TYR 0.020 0.002 TYR C 552 ARG 0.009 0.001 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01900 ( 4) link_NAG-ASN : angle 6.85231 ( 12) link_BETA1-4 : bond 0.01207 ( 4) link_BETA1-4 : angle 3.76663 ( 12) hydrogen bonds : bond 0.04024 ( 482) hydrogen bonds : angle 4.88862 ( 1464) SS BOND : bond 0.00904 ( 4) SS BOND : angle 1.85920 ( 8) covalent geometry : bond 0.00320 (12060) covalent geometry : angle 0.66280 (16424) *********************** 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 284 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 281 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 PHE cc_start: 0.7498 (t80) cc_final: 0.7077 (t80) REVERT: A 675 ARG cc_start: 0.6032 (mtt180) cc_final: 0.5765 (mtt180) REVERT: A 681 TRP cc_start: 0.8722 (t60) cc_final: 0.8474 (t60) REVERT: A 751 GLU cc_start: 0.8276 (pm20) cc_final: 0.8037 (pm20) REVERT: A 754 TYR cc_start: 0.8504 (m-10) cc_final: 0.7975 (m-80) REVERT: A 793 GLN cc_start: 0.5730 (tp40) cc_final: 0.5278 (tp40) REVERT: A 814 MET cc_start: 0.8974 (mtp) cc_final: 0.8752 (mtp) REVERT: A 850 ASP cc_start: 0.5916 (t0) cc_final: 0.5712 (t0) REVERT: B 570 ASP cc_start: 0.7096 (m-30) cc_final: 0.6677 (m-30) REVERT: B 599 LYS cc_start: 0.7102 (ptpp) cc_final: 0.6550 (mmmt) REVERT: B 608 PHE cc_start: 0.6480 (t80) cc_final: 0.6254 (t80) REVERT: B 610 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8465 (mtpp) REVERT: B 700 LEU cc_start: 0.9263 (mm) cc_final: 0.9037 (mm) REVERT: B 767 VAL cc_start: 0.8752 (m) cc_final: 0.8491 (m) REVERT: B 856 LYS cc_start: 0.7702 (tptp) cc_final: 0.6733 (tptt) REVERT: C 630 MET cc_start: 0.8089 (mpp) cc_final: 0.7555 (mpp) REVERT: C 675 ARG cc_start: 0.4831 (mtt180) cc_final: 0.4336 (mtt180) REVERT: C 691 SER cc_start: 0.9100 (m) cc_final: 0.8813 (p) REVERT: C 779 VAL cc_start: 0.9301 (t) cc_final: 0.9071 (t) REVERT: C 843 MET cc_start: 0.5698 (tmm) cc_final: 0.5342 (tmm) REVERT: D 494 LEU cc_start: 0.9010 (tp) cc_final: 0.8727 (tt) REVERT: D 570 ASP cc_start: 0.7746 (m-30) cc_final: 0.7484 (m-30) REVERT: D 608 PHE cc_start: 0.5856 (t80) cc_final: 0.5273 (t80) REVERT: D 610 LYS cc_start: 0.8462 (ttpt) cc_final: 0.7967 (tptp) outliers start: 3 outliers final: 0 residues processed: 283 average time/residue: 0.2035 time to fit residues: 86.0159 Evaluate side-chains 212 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN D 753 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 = 0.3556 r_free = 0.3556 target = 0.085911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068094 restraints weight = 52227.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070289 restraints weight = 33204.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071854 restraints weight = 24132.348| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12072 Z= 0.173 Angle : 0.701 12.826 16456 Z= 0.355 Chirality : 0.050 0.785 1898 Planarity : 0.004 0.043 2072 Dihedral : 7.208 48.197 1766 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1452 helix: -0.23 (0.18), residues: 742 sheet: -2.00 (0.38), residues: 182 loop : -1.86 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 681 HIS 0.011 0.001 HIS A 831 PHE 0.041 0.002 PHE D 564 TYR 0.026 0.002 TYR B 776 ARG 0.007 0.001 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.02240 ( 4) link_NAG-ASN : angle 6.66600 ( 12) link_BETA1-4 : bond 0.01305 ( 4) link_BETA1-4 : angle 3.44587 ( 12) hydrogen bonds : bond 0.03856 ( 482) hydrogen bonds : angle 4.81602 ( 1464) SS BOND : bond 0.00142 ( 4) SS BOND : angle 1.27157 ( 8) covalent geometry : bond 0.00379 (12060) covalent geometry : angle 0.67161 (16424) *********************** 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 272 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 ARG cc_start: 0.6052 (mtt180) cc_final: 0.5785 (mtt180) REVERT: A 751 GLU cc_start: 0.8339 (pm20) cc_final: 0.8064 (pm20) REVERT: A 754 TYR cc_start: 0.8502 (m-10) cc_final: 0.7930 (m-80) REVERT: A 814 MET cc_start: 0.8985 (mtp) cc_final: 0.8771 (mtp) REVERT: B 599 LYS cc_start: 0.7167 (ptpp) cc_final: 0.6511 (mmmt) REVERT: B 608 PHE cc_start: 0.6653 (t80) cc_final: 0.6258 (t80) REVERT: B 610 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8230 (tptp) REVERT: C 562 ASP cc_start: 0.8432 (t0) cc_final: 0.8076 (t70) REVERT: C 630 MET cc_start: 0.8135 (mpp) cc_final: 0.7491 (mpp) REVERT: C 675 ARG cc_start: 0.5065 (mtt180) cc_final: 0.4524 (mtt180) REVERT: C 691 SER cc_start: 0.9102 (m) cc_final: 0.8830 (p) REVERT: C 843 MET cc_start: 0.5598 (tmm) cc_final: 0.5378 (tmm) REVERT: C 861 LEU cc_start: 0.9040 (tp) cc_final: 0.8768 (tt) REVERT: D 494 LEU cc_start: 0.9062 (tp) cc_final: 0.8816 (tt) REVERT: D 570 ASP cc_start: 0.7793 (m-30) cc_final: 0.7447 (m-30) REVERT: D 608 PHE cc_start: 0.5775 (t80) cc_final: 0.5269 (t80) REVERT: D 610 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8022 (tptp) REVERT: D 828 GLU cc_start: 0.8823 (mp0) cc_final: 0.8614 (mp0) REVERT: A 1001 GLU cc_start: 0.6793 (tt0) cc_final: 0.6095 (tt0) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1941 time to fit residues: 79.3726 Evaluate side-chains 196 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** 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** ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068908 restraints weight = 51994.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071150 restraints weight = 33175.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072651 restraints weight = 24152.874| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12072 Z= 0.138 Angle : 0.679 12.631 16456 Z= 0.340 Chirality : 0.048 0.500 1898 Planarity : 0.004 0.046 2072 Dihedral : 6.874 47.565 1766 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1452 helix: 0.04 (0.19), residues: 736 sheet: -1.95 (0.38), residues: 182 loop : -1.75 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 617 HIS 0.009 0.001 HIS A 831 PHE 0.020 0.001 PHE A 626 TYR 0.018 0.002 TYR C 552 ARG 0.006 0.000 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01559 ( 4) link_NAG-ASN : angle 6.33137 ( 12) link_BETA1-4 : bond 0.01049 ( 4) link_BETA1-4 : angle 3.12270 ( 12) hydrogen bonds : bond 0.03577 ( 482) hydrogen bonds : angle 4.69478 ( 1464) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.69250 ( 8) covalent geometry : bond 0.00307 (12060) covalent geometry : angle 0.65099 (16424) *********************** 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 275 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 ARG cc_start: 0.5979 (mtt180) cc_final: 0.5670 (mtt180) REVERT: A 680 ILE cc_start: 0.9192 (mm) cc_final: 0.8981 (mm) REVERT: A 681 TRP cc_start: 0.8657 (t60) cc_final: 0.8255 (t60) REVERT: A 751 GLU cc_start: 0.8302 (pm20) cc_final: 0.8012 (pm20) REVERT: A 754 TYR cc_start: 0.8465 (m-10) cc_final: 0.7889 (m-80) REVERT: A 855 LEU cc_start: 0.7739 (mm) cc_final: 0.7414 (tp) REVERT: B 599 LYS cc_start: 0.7248 (ptpp) cc_final: 0.6535 (mmmt) REVERT: B 608 PHE cc_start: 0.6334 (t80) cc_final: 0.6088 (t80) REVERT: B 610 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8160 (tptp) REVERT: B 630 MET cc_start: 0.7494 (ppp) cc_final: 0.7199 (ppp) REVERT: C 562 ASP cc_start: 0.8432 (t0) cc_final: 0.8042 (t70) REVERT: C 565 ASP cc_start: 0.8472 (m-30) cc_final: 0.8266 (m-30) REVERT: C 630 MET cc_start: 0.8132 (mpp) cc_final: 0.7509 (mpp) REVERT: C 675 ARG cc_start: 0.5148 (mtt180) cc_final: 0.4825 (mtt180) REVERT: C 681 TRP cc_start: 0.8248 (t60) cc_final: 0.7978 (t60) REVERT: C 695 SER cc_start: 0.9090 (m) cc_final: 0.8759 (t) REVERT: C 814 MET cc_start: 0.9232 (mmp) cc_final: 0.9023 (mmp) REVERT: C 861 LEU cc_start: 0.9078 (tp) cc_final: 0.8857 (tt) REVERT: D 494 LEU cc_start: 0.9040 (tp) cc_final: 0.8781 (tt) REVERT: D 518 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7729 (ptm-80) REVERT: D 562 ASP cc_start: 0.8465 (t70) cc_final: 0.8258 (t70) REVERT: D 610 LYS cc_start: 0.8470 (ttpt) cc_final: 0.7957 (tptp) REVERT: D 828 GLU cc_start: 0.8777 (mp0) cc_final: 0.8565 (mp0) REVERT: D 879 ARG cc_start: 0.6858 (tpt-90) cc_final: 0.6385 (mmt90) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2045 time to fit residues: 83.7017 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 : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 0.0040 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.087191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069596 restraints weight = 52079.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071857 restraints weight = 33079.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.073388 restraints weight = 23898.533| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12072 Z= 0.134 Angle : 0.688 12.535 16456 Z= 0.344 Chirality : 0.052 1.071 1898 Planarity : 0.004 0.047 2072 Dihedral : 6.599 45.588 1766 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1452 helix: 0.35 (0.19), residues: 718 sheet: -1.87 (0.39), residues: 182 loop : -1.54 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 681 HIS 0.009 0.001 HIS A 831 PHE 0.018 0.001 PHE C 683 TYR 0.018 0.002 TYR C 754 ARG 0.012 0.000 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01577 ( 4) link_NAG-ASN : angle 7.09908 ( 12) link_BETA1-4 : bond 0.01003 ( 4) link_BETA1-4 : angle 3.70394 ( 12) hydrogen bonds : bond 0.03554 ( 482) hydrogen bonds : angle 4.58177 ( 1464) SS BOND : bond 0.01048 ( 4) SS BOND : angle 2.50531 ( 8) covalent geometry : bond 0.00298 (12060) covalent geometry : angle 0.65168 (16424) *********************** 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 : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7352 (m-80) cc_final: 0.6830 (m-80) REVERT: A 626 PHE cc_start: 0.7701 (t80) cc_final: 0.7495 (t80) REVERT: A 751 GLU cc_start: 0.8193 (pm20) cc_final: 0.7900 (pm20) REVERT: A 754 TYR cc_start: 0.8427 (m-10) cc_final: 0.7799 (m-80) REVERT: A 855 LEU cc_start: 0.7654 (mm) cc_final: 0.7408 (tp) REVERT: A 858 PHE cc_start: 0.8329 (m-10) cc_final: 0.8081 (m-10) REVERT: B 599 LYS cc_start: 0.7338 (ptpp) cc_final: 0.6621 (mmmt) REVERT: B 610 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8171 (tptp) REVERT: B 630 MET cc_start: 0.7584 (ppp) cc_final: 0.7299 (ppp) REVERT: C 592 LEU cc_start: 0.9242 (mt) cc_final: 0.8876 (mt) REVERT: C 630 MET cc_start: 0.8119 (mpp) cc_final: 0.7541 (mpp) REVERT: C 675 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4812 (mtt180) REVERT: C 695 SER cc_start: 0.9011 (m) cc_final: 0.8717 (t) REVERT: D 494 LEU cc_start: 0.9007 (tp) cc_final: 0.8740 (tt) REVERT: D 562 ASP cc_start: 0.8452 (t70) cc_final: 0.8226 (t70) REVERT: D 610 LYS cc_start: 0.8442 (ttpt) cc_final: 0.7928 (tptp) REVERT: D 814 MET cc_start: 0.8918 (mmp) cc_final: 0.8717 (mmp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1877 time to fit residues: 74.5923 Evaluate side-chains 200 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 69 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN B 753 GLN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.086850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.068994 restraints weight = 50800.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071340 restraints weight = 31596.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073013 restraints weight = 22620.691| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6288 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= 0.133 Angle : 0.667 12.468 16456 Z= 0.334 Chirality : 0.049 0.752 1898 Planarity : 0.004 0.046 2072 Dihedral : 6.573 47.169 1766 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.08 % Allowed : 0.79 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1452 helix: 0.41 (0.19), residues: 728 sheet: -1.83 (0.39), residues: 182 loop : -1.53 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 681 HIS 0.009 0.001 HIS A 831 PHE 0.030 0.001 PHE B 608 TYR 0.014 0.001 TYR D 776 ARG 0.007 0.000 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01616 ( 4) link_NAG-ASN : angle 6.64277 ( 12) link_BETA1-4 : bond 0.01003 ( 4) link_BETA1-4 : angle 3.15235 ( 12) hydrogen bonds : bond 0.03429 ( 482) hydrogen bonds : angle 4.51678 ( 1464) SS BOND : bond 0.00147 ( 4) SS BOND : angle 2.06260 ( 8) covalent geometry : bond 0.00297 (12060) covalent geometry : angle 0.63574 (16424) *********************** 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 268 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 1.362 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: 0.7508 (m-80) cc_final: 0.6961 (m-80) REVERT: A 626 PHE cc_start: 0.7776 (t80) cc_final: 0.7482 (t80) REVERT: A 675 ARG cc_start: 0.6349 (mtt180) cc_final: 0.5492 (mtm-85) REVERT: A 680 ILE cc_start: 0.9219 (mm) cc_final: 0.8977 (mm) REVERT: A 751 GLU cc_start: 0.8299 (pm20) cc_final: 0.8020 (pm20) REVERT: A 754 TYR cc_start: 0.8423 (m-10) cc_final: 0.7827 (m-80) REVERT: A 855 LEU cc_start: 0.7618 (mm) cc_final: 0.7391 (tp) REVERT: B 599 LYS cc_start: 0.7368 (ptpp) cc_final: 0.6625 (mmmt) REVERT: B 610 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8388 (mtpp) REVERT: B 630 MET cc_start: 0.7556 (ppp) cc_final: 0.7251 (ppp) REVERT: B 704 GLN cc_start: 0.8523 (mp10) cc_final: 0.8305 (mp10) REVERT: B 753 GLN cc_start: 0.9210 (pt0) cc_final: 0.8754 (pt0) REVERT: B 858 PHE cc_start: 0.6823 (p90) cc_final: 0.6578 (p90) REVERT: C 504 TYR cc_start: 0.8069 (m-80) cc_final: 0.7840 (m-80) REVERT: C 630 MET cc_start: 0.8129 (mpp) cc_final: 0.7535 (mpp) REVERT: C 675 ARG cc_start: 0.5326 (mtt180) cc_final: 0.5012 (mtt180) REVERT: C 695 SER cc_start: 0.9028 (m) cc_final: 0.8751 (t) REVERT: C 814 MET cc_start: 0.9249 (mmp) cc_final: 0.8991 (mmp) REVERT: C 820 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8891 (mt0) REVERT: D 494 LEU cc_start: 0.9045 (tp) cc_final: 0.8774 (tt) REVERT: D 518 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7778 (ptm-80) REVERT: D 610 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7848 (tptp) REVERT: D 814 MET cc_start: 0.8984 (mmp) cc_final: 0.8722 (mmp) outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.2021 time to fit residues: 80.9044 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 : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 725 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 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 = 0.3576 r_free = 0.3576 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069426 restraints weight = 51635.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071685 restraints weight = 32827.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073261 restraints weight = 23901.754| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12072 Z= 0.128 Angle : 0.659 12.423 16456 Z= 0.331 Chirality : 0.048 0.654 1898 Planarity : 0.004 0.047 2072 Dihedral : 6.408 45.151 1766 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1452 helix: 0.47 (0.19), residues: 740 sheet: -1.80 (0.39), residues: 182 loop : -1.67 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 681 HIS 0.005 0.001 HIS A 831 PHE 0.022 0.001 PHE D 626 TYR 0.024 0.001 TYR C 754 ARG 0.008 0.000 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01628 ( 4) link_NAG-ASN : angle 6.49886 ( 12) link_BETA1-4 : bond 0.01099 ( 4) link_BETA1-4 : angle 3.09499 ( 12) hydrogen bonds : bond 0.03381 ( 482) hydrogen bonds : angle 4.50288 ( 1464) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.87438 ( 8) covalent geometry : bond 0.00287 (12060) covalent geometry : angle 0.62928 (16424) *********************** 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 257 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7469 (m-80) cc_final: 0.6975 (m-80) REVERT: A 626 PHE cc_start: 0.7712 (t80) cc_final: 0.7112 (m-80) REVERT: A 751 GLU cc_start: 0.8257 (pm20) cc_final: 0.7997 (pm20) REVERT: A 754 TYR cc_start: 0.8451 (m-10) cc_final: 0.7851 (m-80) REVERT: A 855 LEU cc_start: 0.7558 (mm) cc_final: 0.7321 (tp) REVERT: B 498 VAL cc_start: 0.9261 (t) cc_final: 0.9048 (m) REVERT: B 599 LYS cc_start: 0.7399 (ptpp) cc_final: 0.6635 (mmtt) REVERT: B 610 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8363 (mtpp) REVERT: B 630 MET cc_start: 0.7537 (ppp) cc_final: 0.7261 (ppp) REVERT: C 504 TYR cc_start: 0.8095 (m-80) cc_final: 0.7876 (m-80) REVERT: C 630 MET cc_start: 0.8168 (mpp) cc_final: 0.7550 (mpp) REVERT: C 675 ARG cc_start: 0.5563 (mtt180) cc_final: 0.5230 (mtt180) REVERT: C 695 SER cc_start: 0.9017 (m) cc_final: 0.8745 (t) REVERT: C 709 ILE cc_start: 0.8112 (mm) cc_final: 0.7421 (mm) REVERT: C 715 LEU cc_start: 0.8940 (tt) cc_final: 0.8736 (mt) REVERT: C 814 MET cc_start: 0.9223 (mmp) cc_final: 0.9021 (mmp) REVERT: D 494 LEU cc_start: 0.9047 (tp) cc_final: 0.8767 (tt) REVERT: D 518 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.7750 (ptm-80) REVERT: D 610 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7913 (tptp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1919 time to fit residues: 74.6830 Evaluate side-chains 207 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN A 831 HIS B 725 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.086677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069387 restraints weight = 51603.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071629 restraints weight = 32787.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.073185 restraints weight = 23755.824| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.6652 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= 0.139 Angle : 0.668 12.388 16456 Z= 0.336 Chirality : 0.048 0.640 1898 Planarity : 0.004 0.046 2072 Dihedral : 6.327 43.406 1766 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1452 helix: 0.48 (0.19), residues: 734 sheet: -1.76 (0.40), residues: 182 loop : -1.50 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 617 HIS 0.007 0.001 HIS A 831 PHE 0.020 0.002 PHE D 626 TYR 0.015 0.001 TYR C 552 ARG 0.005 0.000 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.01592 ( 4) link_NAG-ASN : angle 6.50464 ( 12) link_BETA1-4 : bond 0.01082 ( 4) link_BETA1-4 : angle 3.06909 ( 12) hydrogen bonds : bond 0.03333 ( 482) hydrogen bonds : angle 4.55646 ( 1464) SS BOND : bond 0.00126 ( 4) SS BOND : angle 1.90080 ( 8) covalent geometry : bond 0.00312 (12060) covalent geometry : angle 0.63803 (16424) ********************** 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 248 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 TYR cc_start: 0.7376 (m-80) cc_final: 0.6861 (m-80) REVERT: A 570 ASP cc_start: 0.8204 (m-30) cc_final: 0.7379 (m-30) REVERT: A 626 PHE cc_start: 0.7733 (t80) cc_final: 0.7127 (t80) REVERT: A 630 MET cc_start: 0.7912 (mtp) cc_final: 0.7660 (mtt) REVERT: A 680 ILE cc_start: 0.9238 (mm) cc_final: 0.9037 (mm) REVERT: A 751 GLU cc_start: 0.8269 (pm20) cc_final: 0.7978 (pm20) REVERT: A 754 TYR cc_start: 0.8437 (m-10) cc_final: 0.7832 (m-80) REVERT: A 855 LEU cc_start: 0.7554 (mm) cc_final: 0.7344 (tp) REVERT: B 498 VAL cc_start: 0.9246 (t) cc_final: 0.9044 (m) REVERT: B 610 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8337 (mtpp) REVERT: B 630 MET cc_start: 0.7535 (ppp) cc_final: 0.7265 (ppp) REVERT: C 630 MET cc_start: 0.8196 (mpp) cc_final: 0.7573 (mpp) REVERT: C 675 ARG cc_start: 0.5707 (mtt180) cc_final: 0.5194 (mtt180) REVERT: C 695 SER cc_start: 0.9025 (m) cc_final: 0.8783 (t) REVERT: C 814 MET cc_start: 0.9226 (mmp) cc_final: 0.9009 (mmp) REVERT: C 820 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8924 (mt0) REVERT: D 494 LEU cc_start: 0.9084 (tp) cc_final: 0.8815 (tt) REVERT: D 518 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.7748 (ptm-80) REVERT: D 610 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7945 (tptp) REVERT: A 1001 GLU cc_start: 0.7207 (tt0) cc_final: 0.6797 (tt0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2015 time to fit residues: 75.4876 Evaluate side-chains 211 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 725 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067484 restraints weight = 51490.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069693 restraints weight = 32301.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071213 restraints weight = 23365.835| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12072 Z= 0.187 Angle : 0.719 12.282 16456 Z= 0.363 Chirality : 0.050 0.655 1898 Planarity : 0.005 0.047 2072 Dihedral : 6.449 41.743 1766 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1452 helix: 0.37 (0.19), residues: 744 sheet: -1.83 (0.39), residues: 182 loop : -1.66 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 617 HIS 0.001 0.000 HIS A 831 PHE 0.023 0.002 PHE D 626 TYR 0.027 0.002 TYR C 754 ARG 0.005 0.001 ARG C 708 Details of bonding type rmsd link_NAG-ASN : bond 0.01621 ( 4) link_NAG-ASN : angle 6.63048 ( 12) link_BETA1-4 : bond 0.00985 ( 4) link_BETA1-4 : angle 3.05710 ( 12) hydrogen bonds : bond 0.03524 ( 482) hydrogen bonds : angle 4.78617 ( 1464) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.88293 ( 8) covalent geometry : bond 0.00413 (12060) covalent geometry : angle 0.69066 (16424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.40 seconds wall clock time: 64 minutes 34.23 seconds (3874.23 seconds total)