Starting phenix.real_space_refine on Wed Feb 4 18:33:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qpw_53285/02_2026/9qpw_53285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qpw_53285/02_2026/9qpw_53285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qpw_53285/02_2026/9qpw_53285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qpw_53285/02_2026/9qpw_53285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qpw_53285/02_2026/9qpw_53285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qpw_53285/02_2026/9qpw_53285.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 78 5.16 5 C 7828 2.51 5 N 1926 2.21 5 O 2198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12030 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3020 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3011 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 388, 3011 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3067 Chain: "B" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2949 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2949 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3020 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3011 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 388, 3011 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3067 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'E2Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.67, per 1000 atoms: 0.31 Number of scatterers: 12030 At special positions: 0 Unit cell: (101.992, 116.204, 122.892, 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 78 16.00 O 2198 8.00 N 1926 7.00 C 7828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS D 611 " distance=1.92 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS C 611 " distance=2.13 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 884.9 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 18 sheets defined 54.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 438 through 441 removed outlier: 3.790A pdb=" N ASP A 441 " --> pdb=" O GLU A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.626A pdb=" N SER A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 544 through 565 removed outlier: 3.714A pdb=" N TRP A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 608 Processing helix chain 'A' and resid 617 through 652 removed outlier: 3.825A pdb=" N VAL A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.718A pdb=" N GLN A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 683 removed outlier: 4.188A pdb=" N GLU A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 707 through 717 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 765 through 779 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 814 through 836 removed outlier: 3.681A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 441 removed outlier: 3.821A pdb=" N ASP B 441 " --> pdb=" O GLU B 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 441' Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 504 through 510 removed outlier: 3.965A pdb=" N VAL B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.819A pdb=" N LEU B 540 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 541 " --> pdb=" O SER B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 541' Processing helix chain 'B' and resid 544 through 567 Processing helix chain 'B' and resid 598 through 607 Processing helix chain 'B' and resid 617 through 648 removed outlier: 4.227A pdb=" N VAL B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 624 " --> pdb=" O GLY B 620 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP B 627 " --> pdb=" O VAL B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.590A pdb=" N LEU B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 683 removed outlier: 3.740A pdb=" N GLU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 698 Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.726A pdb=" N GLY B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 716 " --> pdb=" O VAL B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 764 through 779 Processing helix chain 'B' and resid 779 through 791 removed outlier: 3.543A pdb=" N LYS B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 836 removed outlier: 4.258A pdb=" N VAL B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY B 816 " --> pdb=" O SER B 812 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 441 removed outlier: 3.822A pdb=" N ASP D 441 " --> pdb=" O GLU D 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 441' Processing helix chain 'D' and resid 445 through 459 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 504 through 510 removed outlier: 3.965A pdb=" N VAL D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 removed outlier: 3.820A pdb=" N LEU D 540 " --> pdb=" O PHE D 537 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP D 541 " --> pdb=" O SER D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 537 through 541' Processing helix chain 'D' and resid 544 through 567 Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 617 through 648 removed outlier: 4.228A pdb=" N VAL D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 624 " --> pdb=" O GLY D 620 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP D 627 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 664 removed outlier: 3.590A pdb=" N LEU D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 removed outlier: 3.739A pdb=" N GLU D 679 " --> pdb=" O GLY D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 698 Processing helix chain 'D' and resid 707 through 718 removed outlier: 3.726A pdb=" N GLY D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 716 " --> pdb=" O VAL D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 736 Processing helix chain 'D' and resid 764 through 779 Processing helix chain 'D' and resid 779 through 791 removed outlier: 3.544A pdb=" N LYS D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 836 removed outlier: 4.258A pdb=" N VAL D 814 " --> pdb=" O SER D 810 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY D 816 " --> pdb=" O SER D 812 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 817 " --> pdb=" O ASN D 813 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 830 " --> pdb=" O GLY D 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 441 removed outlier: 3.790A pdb=" N ASP C 441 " --> pdb=" O GLU C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.624A pdb=" N SER C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 544 through 565 removed outlier: 3.715A pdb=" N TRP C 548 " --> pdb=" O ALA C 544 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C 553 " --> pdb=" O MET C 549 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 608 Processing helix chain 'C' and resid 617 through 652 removed outlier: 3.825A pdb=" N VAL C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 664 removed outlier: 3.718A pdb=" N GLN C 664 " --> pdb=" O ASP C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 683 removed outlier: 4.189A pdb=" N GLU C 679 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE C 681 " --> pdb=" O THR C 677 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 699 Processing helix chain 'C' and resid 707 through 717 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 765 through 779 Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 811 through 813 No H-bonds generated for 'chain 'C' and resid 811 through 813' Processing helix chain 'C' and resid 814 through 836 removed outlier: 3.674A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 830 " --> pdb=" O GLY C 826 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421 removed outlier: 6.579A pdb=" N VAL A 417 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 465 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 419 " --> pdb=" O ALA A 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 499 removed outlier: 4.700A pdb=" N ALA A 499 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY A 755 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 668 through 670 removed outlier: 6.612A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 417 through 421 removed outlier: 6.046A pdb=" N VAL B 417 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 465 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 419 " --> pdb=" O ALA B 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA7, first strand: chain 'B' and resid 497 through 502 removed outlier: 9.602A pdb=" N ALA B 497 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA B 499 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA B 757 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 501 " --> pdb=" O GLY B 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 524 through 527 removed outlier: 3.979A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 745 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 668 through 670 Processing sheet with id=AB1, first strand: chain 'D' and resid 417 through 421 removed outlier: 6.046A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA D 465 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL D 419 " --> pdb=" O ALA D 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB3, first strand: chain 'D' and resid 497 through 502 removed outlier: 9.603A pdb=" N ALA D 497 " --> pdb=" O PRO D 759 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA D 499 " --> pdb=" O ALA D 757 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA D 757 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU D 501 " --> pdb=" O GLY D 755 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 524 through 527 removed outlier: 3.979A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 745 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 668 through 670 Processing sheet with id=AB6, first strand: chain 'C' and resid 417 through 421 removed outlier: 6.579A pdb=" N VAL C 417 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA C 465 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL C 419 " --> pdb=" O ALA C 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB8, first strand: chain 'C' and resid 497 through 499 removed outlier: 4.700A pdb=" N ALA C 499 " --> pdb=" O GLY C 755 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY C 755 " --> pdb=" O ALA C 499 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 668 through 670 removed outlier: 6.612A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1713 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: 2.08 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2913 1.33 - 1.46: 3776 1.46 - 1.59: 5477 1.59 - 1.72: 4 1.72 - 1.84: 134 Bond restraints: 12304 Sorted by residual: bond pdb=" C08 E2Q D1001 " pdb=" C09 E2Q D1001 " ideal model delta sigma weight residual 1.422 1.489 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C08 E2Q B1001 " pdb=" C09 E2Q B1001 " ideal model delta sigma weight residual 1.422 1.488 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C07 E2Q D1001 " pdb=" C08 E2Q D1001 " ideal model delta sigma weight residual 1.423 1.472 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C07 E2Q B1001 " pdb=" C08 E2Q B1001 " ideal model delta sigma weight residual 1.423 1.471 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C08 E2Q C1001 " pdb=" C09 E2Q C1001 " ideal model delta sigma weight residual 1.422 1.466 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 12299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16464 2.24 - 4.47: 181 4.47 - 6.71: 13 6.71 - 8.95: 0 8.95 - 11.18: 2 Bond angle restraints: 16660 Sorted by residual: angle pdb=" CA CYS B 611 " pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " ideal model delta sigma weight residual 114.40 125.58 -11.18 2.30e+00 1.89e-01 2.36e+01 angle pdb=" CA CYS D 611 " pdb=" CB CYS D 611 " pdb=" SG CYS D 611 " ideal model delta sigma weight residual 114.40 125.56 -11.16 2.30e+00 1.89e-01 2.35e+01 angle pdb=" C CYS B 611 " pdb=" CA CYS B 611 " pdb=" CB CYS B 611 " ideal model delta sigma weight residual 109.80 113.93 -4.13 1.64e+00 3.72e-01 6.34e+00 angle pdb=" C CYS D 611 " pdb=" CA CYS D 611 " pdb=" CB CYS D 611 " ideal model delta sigma weight residual 109.80 113.92 -4.12 1.64e+00 3.72e-01 6.31e+00 angle pdb=" C THR C 705 " pdb=" N ARG C 706 " pdb=" CA ARG C 706 " ideal model delta sigma weight residual 120.38 123.52 -3.14 1.37e+00 5.33e-01 5.26e+00 ... (remaining 16655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.48: 6718 12.48 - 24.97: 427 24.97 - 37.45: 110 37.45 - 49.93: 21 49.93 - 62.42: 12 Dihedral angle restraints: 7288 sinusoidal: 2872 harmonic: 4416 Sorted by residual: dihedral pdb=" CB CYS A 611 " pdb=" SG CYS A 611 " pdb=" SG CYS D 611 " pdb=" CB CYS D 611 " ideal model delta sinusoidal sigma weight residual -86.00 -125.72 39.72 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS C 611 " pdb=" CB CYS C 611 " ideal model delta sinusoidal sigma weight residual -86.00 -124.20 38.20 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" SG CYS C 740 " pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" CA CYS C 795 " ideal model delta sinusoidal sigma weight residual -177.00 -125.37 -51.63 1 2.00e+01 2.50e-03 9.10e+00 ... (remaining 7285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1490 0.048 - 0.096: 292 0.096 - 0.145: 83 0.145 - 0.193: 3 0.193 - 0.241: 2 Chirality restraints: 1870 Sorted by residual: chirality pdb=" CB ILE B 496 " pdb=" CA ILE B 496 " pdb=" CG1 ILE B 496 " pdb=" CG2 ILE B 496 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE D 496 " pdb=" CA ILE D 496 " pdb=" CG1 ILE D 496 " pdb=" CG2 ILE D 496 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB THR C 420 " pdb=" CA THR C 420 " pdb=" OG1 THR C 420 " pdb=" CG2 THR C 420 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 1867 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 E2Q B1001 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" N15 E2Q B1001 " -0.063 2.00e-02 2.50e+03 pdb=" O16 E2Q B1001 " 0.022 2.00e-02 2.50e+03 pdb=" O17 E2Q B1001 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 E2Q D1001 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" N15 E2Q D1001 " 0.062 2.00e-02 2.50e+03 pdb=" O16 E2Q D1001 " -0.022 2.00e-02 2.50e+03 pdb=" O17 E2Q D1001 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 716 " 0.234 9.50e-02 1.11e+02 1.06e-01 8.88e+00 pdb=" NE ARG C 716 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG C 716 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG C 716 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 716 " 0.000 2.00e-02 2.50e+03 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2044 2.77 - 3.30: 11944 3.30 - 3.83: 19535 3.83 - 4.37: 23375 4.37 - 4.90: 39711 Nonbonded interactions: 96609 Sorted by model distance: nonbonded pdb=" N14 E2Q D1001 " pdb=" O17 E2Q D1001 " model vdw 2.232 3.120 nonbonded pdb=" N14 E2Q B1001 " pdb=" O17 E2Q B1001 " model vdw 2.233 3.120 nonbonded pdb=" OG SER D 538 " pdb=" O ASN D 813 " model vdw 2.262 3.040 nonbonded pdb=" OG SER B 538 " pdb=" O ASN B 813 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP D 449 " pdb=" NE1 TRP D 788 " model vdw 2.315 3.120 ... (remaining 96604 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.730 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.003 0.107 12308 Z= 0.155 Angle : 0.568 11.182 16668 Z= 0.295 Chirality : 0.041 0.241 1870 Planarity : 0.008 0.106 2046 Dihedral : 9.156 62.416 4456 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1512 helix: -1.07 (0.18), residues: 774 sheet: -2.02 (0.49), residues: 108 loop : -2.40 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.004 ARG C 716 TYR 0.018 0.001 TYR D 443 PHE 0.013 0.001 PHE C 539 TRP 0.017 0.001 TRP B 693 HIS 0.001 0.000 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00291 (12304) covalent geometry : angle 0.55997 (16660) SS BOND : bond 0.07380 ( 4) SS BOND : angle 4.38019 ( 8) hydrogen bonds : bond 0.26002 ( 577) hydrogen bonds : angle 7.96315 ( 1713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.413 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 430 TYR cc_start: 0.5881 (m-80) cc_final: 0.5659 (m-80) REVERT: A 523 SER cc_start: 0.9146 (p) cc_final: 0.8743 (t) REVERT: B 443 TYR cc_start: 0.6980 (m-10) cc_final: 0.6558 (m-80) REVERT: B 563 PHE cc_start: 0.7332 (t80) cc_final: 0.6917 (m-10) REVERT: B 564 LEU cc_start: 0.8320 (mt) cc_final: 0.8115 (mp) REVERT: B 655 ILE cc_start: 0.8991 (mm) cc_final: 0.8761 (mp) REVERT: B 788 TRP cc_start: 0.8327 (m100) cc_final: 0.8086 (m100) REVERT: D 443 TYR cc_start: 0.6935 (m-10) cc_final: 0.6540 (m-80) REVERT: D 563 PHE cc_start: 0.7212 (t80) cc_final: 0.6917 (m-10) REVERT: D 788 TRP cc_start: 0.8313 (m100) cc_final: 0.8095 (m100) REVERT: C 664 GLN cc_start: 0.7857 (pp30) cc_final: 0.7520 (pp30) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1299 time to fit residues: 65.0388 Evaluate side-chains 199 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122905 restraints weight = 35530.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123793 restraints weight = 32769.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125005 restraints weight = 24653.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126126 restraints weight = 17426.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126473 restraints weight = 16022.876| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12308 Z= 0.172 Angle : 0.655 7.983 16668 Z= 0.330 Chirality : 0.045 0.276 1870 Planarity : 0.004 0.042 2046 Dihedral : 5.637 48.516 1704 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.33 % Allowed : 11.33 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1512 helix: 1.19 (0.19), residues: 788 sheet: -1.32 (0.45), residues: 136 loop : -1.50 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 697 TYR 0.014 0.002 TYR A 669 PHE 0.028 0.002 PHE B 539 TRP 0.015 0.002 TRP D 627 HIS 0.006 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00399 (12304) covalent geometry : angle 0.65302 (16660) SS BOND : bond 0.00278 ( 4) SS BOND : angle 2.59049 ( 8) hydrogen bonds : bond 0.04399 ( 577) hydrogen bonds : angle 4.60346 ( 1713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.401 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 423 MET cc_start: 0.7369 (tpp) cc_final: 0.6857 (mpp) REVERT: A 523 SER cc_start: 0.9404 (p) cc_final: 0.9106 (t) REVERT: B 440 ASN cc_start: 0.8294 (m-40) cc_final: 0.7944 (m-40) REVERT: B 525 MET cc_start: 0.8819 (tpp) cc_final: 0.8144 (ttt) REVERT: B 563 PHE cc_start: 0.7411 (t80) cc_final: 0.6941 (m-80) REVERT: B 829 MET cc_start: 0.7542 (mmm) cc_final: 0.7240 (mmm) REVERT: D 485 MET cc_start: 0.8082 (mtm) cc_final: 0.7822 (mtp) REVERT: D 525 MET cc_start: 0.8821 (tpp) cc_final: 0.8115 (ttt) REVERT: D 563 PHE cc_start: 0.7276 (t80) cc_final: 0.6902 (m-80) REVERT: D 829 MET cc_start: 0.7506 (mmm) cc_final: 0.7160 (mmm) REVERT: C 552 VAL cc_start: 0.8775 (p) cc_final: 0.8565 (t) outliers start: 17 outliers final: 12 residues processed: 231 average time/residue: 0.1060 time to fit residues: 36.0206 Evaluate side-chains 197 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 764 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 123 optimal weight: 0.0040 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120178 restraints weight = 31972.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122148 restraints weight = 24879.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123906 restraints weight = 19048.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124383 restraints weight = 13301.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125000 restraints weight = 13315.597| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12308 Z= 0.126 Angle : 0.579 8.867 16668 Z= 0.287 Chirality : 0.041 0.167 1870 Planarity : 0.004 0.045 2046 Dihedral : 5.886 59.642 1704 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 1.95 % Allowed : 12.50 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1512 helix: 1.73 (0.19), residues: 790 sheet: -1.24 (0.44), residues: 140 loop : -1.26 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 697 TYR 0.009 0.001 TYR B 491 PHE 0.017 0.001 PHE B 539 TRP 0.031 0.001 TRP D 788 HIS 0.002 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00285 (12304) covalent geometry : angle 0.57638 (16660) SS BOND : bond 0.01135 ( 4) SS BOND : angle 2.53443 ( 8) hydrogen bonds : bond 0.03798 ( 577) hydrogen bonds : angle 4.27553 ( 1713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7404 (tpp) cc_final: 0.6916 (mpp) REVERT: A 523 SER cc_start: 0.9372 (p) cc_final: 0.9075 (t) REVERT: B 525 MET cc_start: 0.8881 (tpp) cc_final: 0.8298 (ttt) REVERT: B 563 PHE cc_start: 0.7335 (t80) cc_final: 0.6894 (m-80) REVERT: B 829 MET cc_start: 0.7626 (mmm) cc_final: 0.7317 (mmm) REVERT: D 485 MET cc_start: 0.8013 (mtm) cc_final: 0.7729 (mtp) REVERT: D 525 MET cc_start: 0.8874 (tpp) cc_final: 0.8241 (ttt) REVERT: D 563 PHE cc_start: 0.7214 (t80) cc_final: 0.6851 (m-80) REVERT: C 423 MET cc_start: 0.7017 (mmm) cc_final: 0.6588 (mmm) outliers start: 25 outliers final: 16 residues processed: 230 average time/residue: 0.1088 time to fit residues: 36.4136 Evaluate side-chains 202 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 764 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 137 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116229 restraints weight = 23654.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117317 restraints weight = 19413.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118965 restraints weight = 16119.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119467 restraints weight = 12127.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119748 restraints weight = 11274.168| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12308 Z= 0.180 Angle : 0.624 8.050 16668 Z= 0.314 Chirality : 0.044 0.205 1870 Planarity : 0.004 0.037 2046 Dihedral : 6.079 57.428 1704 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.31 % Favored : 96.56 % Rotamer: Outliers : 2.03 % Allowed : 13.52 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1512 helix: 1.63 (0.19), residues: 788 sheet: -1.77 (0.41), residues: 160 loop : -1.01 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 697 TYR 0.010 0.001 TYR C 443 PHE 0.026 0.002 PHE A 517 TRP 0.048 0.002 TRP D 788 HIS 0.004 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00424 (12304) covalent geometry : angle 0.62184 (16660) SS BOND : bond 0.00357 ( 4) SS BOND : angle 2.37225 ( 8) hydrogen bonds : bond 0.03798 ( 577) hydrogen bonds : angle 4.34303 ( 1713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7608 (tpp) cc_final: 0.7139 (mpp) REVERT: A 523 SER cc_start: 0.9389 (p) cc_final: 0.9118 (t) REVERT: B 525 MET cc_start: 0.8929 (tpp) cc_final: 0.8386 (ttt) REVERT: B 563 PHE cc_start: 0.7376 (t80) cc_final: 0.6853 (m-80) REVERT: B 829 MET cc_start: 0.7552 (mmm) cc_final: 0.7232 (mmm) REVERT: D 525 MET cc_start: 0.8874 (tpp) cc_final: 0.8392 (ttt) REVERT: D 563 PHE cc_start: 0.7231 (t80) cc_final: 0.6848 (m-80) REVERT: D 651 MET cc_start: 0.6566 (mtt) cc_final: 0.6235 (mtt) REVERT: C 811 LEU cc_start: 0.9200 (mt) cc_final: 0.8993 (mt) outliers start: 26 outliers final: 19 residues processed: 208 average time/residue: 0.0991 time to fit residues: 29.9808 Evaluate side-chains 194 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113040 restraints weight = 32267.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115384 restraints weight = 25967.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116917 restraints weight = 18489.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117440 restraints weight = 13702.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117864 restraints weight = 12612.020| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12308 Z= 0.200 Angle : 0.637 7.687 16668 Z= 0.320 Chirality : 0.044 0.156 1870 Planarity : 0.004 0.040 2046 Dihedral : 6.179 59.612 1704 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.34 % Allowed : 14.14 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1512 helix: 1.45 (0.19), residues: 790 sheet: -1.70 (0.42), residues: 154 loop : -1.03 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 697 TYR 0.014 0.002 TYR A 819 PHE 0.027 0.002 PHE C 517 TRP 0.061 0.002 TRP B 788 HIS 0.004 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00474 (12304) covalent geometry : angle 0.63568 (16660) SS BOND : bond 0.00438 ( 4) SS BOND : angle 2.28733 ( 8) hydrogen bonds : bond 0.03841 ( 577) hydrogen bonds : angle 4.33731 ( 1713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7657 (tpp) cc_final: 0.7224 (mpp) REVERT: A 523 SER cc_start: 0.9422 (p) cc_final: 0.9115 (t) REVERT: A 609 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7673 (mp-120) REVERT: B 525 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8699 (ttt) REVERT: B 563 PHE cc_start: 0.7436 (t80) cc_final: 0.6797 (m-80) REVERT: B 829 MET cc_start: 0.7669 (mmm) cc_final: 0.7383 (mmm) REVERT: D 433 ASN cc_start: 0.7562 (p0) cc_final: 0.7292 (p0) REVERT: D 437 PHE cc_start: 0.7611 (m-80) cc_final: 0.7405 (m-80) REVERT: D 525 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8706 (ttt) REVERT: D 563 PHE cc_start: 0.7325 (t80) cc_final: 0.6827 (m-80) REVERT: D 829 MET cc_start: 0.7744 (mmm) cc_final: 0.7246 (mmt) outliers start: 30 outliers final: 21 residues processed: 187 average time/residue: 0.0996 time to fit residues: 27.4141 Evaluate side-chains 180 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 0.0060 chunk 35 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 47 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117978 restraints weight = 23689.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118914 restraints weight = 18979.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119817 restraints weight = 15683.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120799 restraints weight = 12780.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120945 restraints weight = 11689.251| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12308 Z= 0.109 Angle : 0.568 8.169 16668 Z= 0.279 Chirality : 0.041 0.154 1870 Planarity : 0.003 0.031 2046 Dihedral : 6.129 59.246 1704 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.56 % Allowed : 15.16 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1512 helix: 1.72 (0.19), residues: 802 sheet: -1.70 (0.41), residues: 158 loop : -0.87 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 682 TYR 0.009 0.001 TYR C 472 PHE 0.014 0.001 PHE D 539 TRP 0.063 0.002 TRP D 788 HIS 0.001 0.000 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00244 (12304) covalent geometry : angle 0.56631 (16660) SS BOND : bond 0.00172 ( 4) SS BOND : angle 2.22346 ( 8) hydrogen bonds : bond 0.03117 ( 577) hydrogen bonds : angle 4.06951 ( 1713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7553 (tpp) cc_final: 0.7338 (mmm) REVERT: A 523 SER cc_start: 0.9365 (p) cc_final: 0.9084 (t) REVERT: A 609 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7543 (mp-120) REVERT: B 437 PHE cc_start: 0.7423 (m-80) cc_final: 0.7217 (m-80) REVERT: B 525 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8452 (ttt) REVERT: B 563 PHE cc_start: 0.7317 (t80) cc_final: 0.6742 (m-80) REVERT: B 656 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 820 ILE cc_start: 0.7547 (tt) cc_final: 0.6718 (mt) REVERT: B 829 MET cc_start: 0.7711 (mmm) cc_final: 0.7438 (mmm) REVERT: D 433 ASN cc_start: 0.7438 (p0) cc_final: 0.7035 (p0) REVERT: D 437 PHE cc_start: 0.7506 (m-80) cc_final: 0.7129 (m-80) REVERT: D 485 MET cc_start: 0.7896 (mtm) cc_final: 0.7567 (mtp) REVERT: D 525 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8473 (ttt) REVERT: D 563 PHE cc_start: 0.7195 (t80) cc_final: 0.6815 (m-80) REVERT: D 651 MET cc_start: 0.6668 (mtt) cc_final: 0.6369 (mtt) REVERT: C 485 MET cc_start: 0.7650 (ptt) cc_final: 0.7335 (ptt) REVERT: C 609 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: C 649 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6921 (mm-30) outliers start: 20 outliers final: 5 residues processed: 190 average time/residue: 0.0968 time to fit residues: 27.1795 Evaluate side-chains 169 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116419 restraints weight = 30530.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119117 restraints weight = 24100.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120343 restraints weight = 17796.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120713 restraints weight = 13242.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121229 restraints weight = 12150.652| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12308 Z= 0.142 Angle : 0.590 8.304 16668 Z= 0.292 Chirality : 0.043 0.320 1870 Planarity : 0.004 0.036 2046 Dihedral : 6.151 59.276 1704 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.64 % Allowed : 15.31 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1512 helix: 1.76 (0.19), residues: 788 sheet: -1.68 (0.41), residues: 160 loop : -0.85 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 683 TYR 0.009 0.001 TYR B 555 PHE 0.018 0.002 PHE C 517 TRP 0.068 0.002 TRP D 788 HIS 0.002 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00337 (12304) covalent geometry : angle 0.58897 (16660) SS BOND : bond 0.00141 ( 4) SS BOND : angle 1.89222 ( 8) hydrogen bonds : bond 0.03334 ( 577) hydrogen bonds : angle 4.08072 ( 1713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 SER cc_start: 0.9415 (p) cc_final: 0.9108 (t) REVERT: A 609 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7651 (mp-120) REVERT: B 437 PHE cc_start: 0.7429 (m-80) cc_final: 0.7192 (m-80) REVERT: B 525 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8669 (ttt) REVERT: B 563 PHE cc_start: 0.7376 (t80) cc_final: 0.6770 (m-80) REVERT: B 820 ILE cc_start: 0.7556 (tt) cc_final: 0.6706 (mt) REVERT: B 829 MET cc_start: 0.7688 (mmm) cc_final: 0.7429 (mmm) REVERT: D 437 PHE cc_start: 0.7596 (m-80) cc_final: 0.7339 (m-80) REVERT: D 485 MET cc_start: 0.8057 (mtm) cc_final: 0.7784 (mtp) REVERT: D 525 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8666 (ttt) REVERT: D 563 PHE cc_start: 0.7247 (t80) cc_final: 0.6840 (m-80) REVERT: D 820 ILE cc_start: 0.7477 (tt) cc_final: 0.6710 (mt) REVERT: D 829 MET cc_start: 0.7934 (mmm) cc_final: 0.7676 (mmm) REVERT: C 649 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6917 (mm-30) outliers start: 21 outliers final: 12 residues processed: 181 average time/residue: 0.1047 time to fit residues: 27.9924 Evaluate side-chains 174 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 91 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 123 optimal weight: 0.0010 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 0.1980 chunk 83 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120922 restraints weight = 29747.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122217 restraints weight = 26433.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123446 restraints weight = 21673.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124236 restraints weight = 15489.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124535 restraints weight = 14420.725| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12308 Z= 0.106 Angle : 0.572 9.000 16668 Z= 0.279 Chirality : 0.041 0.245 1870 Planarity : 0.003 0.032 2046 Dihedral : 6.137 59.354 1704 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.48 % Allowed : 15.16 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1512 helix: 1.95 (0.19), residues: 788 sheet: -1.46 (0.41), residues: 170 loop : -0.78 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 621 TYR 0.010 0.001 TYR C 819 PHE 0.015 0.001 PHE B 539 TRP 0.051 0.002 TRP D 788 HIS 0.002 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00241 (12304) covalent geometry : angle 0.57105 (16660) SS BOND : bond 0.00082 ( 4) SS BOND : angle 1.53033 ( 8) hydrogen bonds : bond 0.02926 ( 577) hydrogen bonds : angle 3.94782 ( 1713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 SER cc_start: 0.9409 (p) cc_final: 0.9091 (t) REVERT: B 437 PHE cc_start: 0.7339 (m-80) cc_final: 0.7123 (m-80) REVERT: B 496 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 525 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8391 (ttt) REVERT: B 563 PHE cc_start: 0.7271 (t80) cc_final: 0.6797 (m-80) REVERT: B 820 ILE cc_start: 0.7371 (tt) cc_final: 0.6534 (mt) REVERT: B 829 MET cc_start: 0.7731 (mmm) cc_final: 0.7461 (mmm) REVERT: D 485 MET cc_start: 0.7900 (mtm) cc_final: 0.7647 (mtp) REVERT: D 496 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7908 (mm) REVERT: D 525 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8411 (ttt) REVERT: D 563 PHE cc_start: 0.7182 (t80) cc_final: 0.6930 (m-10) REVERT: D 820 ILE cc_start: 0.7241 (tt) cc_final: 0.6486 (mt) REVERT: C 485 MET cc_start: 0.7655 (ptt) cc_final: 0.7053 (ptt) REVERT: C 649 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6900 (mm-30) REVERT: C 748 ASN cc_start: 0.7752 (m-40) cc_final: 0.7540 (m-40) outliers start: 19 outliers final: 9 residues processed: 191 average time/residue: 0.1121 time to fit residues: 30.8186 Evaluate side-chains 183 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 114 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116103 restraints weight = 24621.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116989 restraints weight = 20839.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118783 restraints weight = 17255.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119307 restraints weight = 12719.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119658 restraints weight = 11685.784| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12308 Z= 0.141 Angle : 0.611 9.109 16668 Z= 0.295 Chirality : 0.043 0.225 1870 Planarity : 0.003 0.031 2046 Dihedral : 6.204 59.657 1704 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.33 % Allowed : 15.31 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1512 helix: 1.91 (0.19), residues: 788 sheet: -1.63 (0.41), residues: 160 loop : -0.81 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 621 TYR 0.019 0.001 TYR A 819 PHE 0.018 0.002 PHE C 517 TRP 0.046 0.002 TRP D 788 HIS 0.002 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00333 (12304) covalent geometry : angle 0.61020 (16660) SS BOND : bond 0.00123 ( 4) SS BOND : angle 1.59342 ( 8) hydrogen bonds : bond 0.03182 ( 577) hydrogen bonds : angle 4.05045 ( 1713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 SER cc_start: 0.9376 (p) cc_final: 0.9078 (t) REVERT: B 437 PHE cc_start: 0.7453 (m-80) cc_final: 0.7242 (m-80) REVERT: B 525 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8667 (ttt) REVERT: B 563 PHE cc_start: 0.7374 (t80) cc_final: 0.6783 (m-80) REVERT: B 820 ILE cc_start: 0.7505 (tt) cc_final: 0.6691 (mt) REVERT: B 829 MET cc_start: 0.7761 (mmm) cc_final: 0.7514 (mmm) REVERT: D 525 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8664 (ttt) REVERT: D 563 PHE cc_start: 0.7258 (t80) cc_final: 0.6902 (m-10) REVERT: D 820 ILE cc_start: 0.7332 (tt) cc_final: 0.6556 (mt) REVERT: C 649 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6904 (mm-30) outliers start: 17 outliers final: 13 residues processed: 177 average time/residue: 0.1113 time to fit residues: 28.9245 Evaluate side-chains 177 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 525 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114786 restraints weight = 41333.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118450 restraints weight = 36361.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119475 restraints weight = 20598.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120087 restraints weight = 16687.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120763 restraints weight = 15978.564| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12308 Z= 0.150 Angle : 0.624 9.780 16668 Z= 0.302 Chirality : 0.042 0.183 1870 Planarity : 0.003 0.030 2046 Dihedral : 6.261 59.534 1704 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.33 % Allowed : 15.47 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1512 helix: 1.82 (0.19), residues: 802 sheet: -1.65 (0.41), residues: 160 loop : -0.78 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 621 TYR 0.022 0.001 TYR A 819 PHE 0.019 0.002 PHE A 537 TRP 0.034 0.001 TRP D 788 HIS 0.002 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00357 (12304) covalent geometry : angle 0.62311 (16660) SS BOND : bond 0.00145 ( 4) SS BOND : angle 1.68403 ( 8) hydrogen bonds : bond 0.03256 ( 577) hydrogen bonds : angle 4.07606 ( 1713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 SER cc_start: 0.9396 (p) cc_final: 0.9092 (t) REVERT: B 525 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8668 (ttt) REVERT: B 563 PHE cc_start: 0.7339 (t80) cc_final: 0.6829 (m-80) REVERT: B 820 ILE cc_start: 0.7560 (tt) cc_final: 0.6713 (mt) REVERT: B 829 MET cc_start: 0.7707 (mmm) cc_final: 0.7446 (mmm) REVERT: D 525 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8660 (ttt) REVERT: D 563 PHE cc_start: 0.7217 (t80) cc_final: 0.6948 (m-10) REVERT: C 485 MET cc_start: 0.7733 (ptt) cc_final: 0.7458 (ptt) REVERT: C 607 MET cc_start: 0.8254 (mmt) cc_final: 0.7843 (mmm) REVERT: C 649 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6922 (mm-30) outliers start: 17 outliers final: 15 residues processed: 176 average time/residue: 0.0971 time to fit residues: 25.1615 Evaluate side-chains 179 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 751 SER Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 525 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 617 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 100 optimal weight: 0.0030 chunk 11 optimal weight: 0.4980 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 434 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120002 restraints weight = 27764.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121025 restraints weight = 26139.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122388 restraints weight = 21509.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123083 restraints weight = 15376.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123409 restraints weight = 14428.631| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12308 Z= 0.117 Angle : 0.612 10.772 16668 Z= 0.294 Chirality : 0.041 0.152 1870 Planarity : 0.003 0.029 2046 Dihedral : 6.291 59.637 1704 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.09 % Allowed : 15.78 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1512 helix: 1.93 (0.19), residues: 802 sheet: -1.62 (0.41), residues: 160 loop : -0.81 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 621 TYR 0.022 0.001 TYR A 819 PHE 0.014 0.001 PHE B 539 TRP 0.025 0.001 TRP B 788 HIS 0.002 0.000 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00272 (12304) covalent geometry : angle 0.61082 (16660) SS BOND : bond 0.00590 ( 4) SS BOND : angle 1.90801 ( 8) hydrogen bonds : bond 0.03045 ( 577) hydrogen bonds : angle 4.00568 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.08 seconds wall clock time: 34 minutes 31.76 seconds (2071.76 seconds total)