Starting phenix.real_space_refine on Sun Aug 24 07:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ksl_23019/08_2025/7ksl_23019.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ksl_23019/08_2025/7ksl_23019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ksl_23019/08_2025/7ksl_23019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ksl_23019/08_2025/7ksl_23019.map" model { file = "/net/cci-nas-00/data/ceres_data/7ksl_23019/08_2025/7ksl_23019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ksl_23019/08_2025/7ksl_23019.cif" } resolution = 3.5 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= 0.045 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 87 5.16 5 C 11611 2.51 5 N 3162 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18306 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3291 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 11, 'GLU:plan': 22, 'HIS:plan': 3, 'ASP:plan': 18, 'ASN:plan1': 6, 'TYR:plan': 5, 'TRP:plan': 2, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3770 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 7, 'GLU:plan': 17, 'ASP:plan': 13, 'ASN:plan1': 1, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 177 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3826 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 6, 'GLU:plan': 14, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 141 Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3881 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3403 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 16, 'GLU:plan': 21, 'HIS:plan': 5, 'ASP:plan': 15, 'ASN:plan1': 8, 'TRP:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.22 Number of scatterers: 18306 At special positions: 0 Unit cell: (117.3, 132.25, 132.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 10 15.00 O 3436 8.00 N 3162 7.00 C 11611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.40 Conformation dependent library (CDL) restraints added in 775.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 23 sheets defined 48.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 421 through 428 Processing helix chain 'C' and resid 431 through 447 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 557 through 558 No H-bonds generated for 'chain 'C' and resid 557 through 558' Processing helix chain 'C' and resid 571 through 571 No H-bonds generated for 'chain 'C' and resid 571 through 571' Processing helix chain 'C' and resid 572 through 581 Processing helix chain 'C' and resid 604 through 611 Processing helix chain 'C' and resid 612 through 617 Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 852 through 855 Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 924 through 929 removed outlier: 3.795A pdb=" N THR C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 946 removed outlier: 3.976A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.879A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 4.364A pdb=" N VAL B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 592 through 595 removed outlier: 3.861A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.722A pdb=" N THR B 644 " --> pdb=" O VAL B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.545A pdb=" N GLN B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 855 removed outlier: 3.584A pdb=" N SER B 855 " --> pdb=" O ASP B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 904 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.906A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.904A pdb=" N LEU A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.943A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 591 through 595 removed outlier: 4.133A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.907A pdb=" N THR A 644 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 4.310A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 682 removed outlier: 4.890A pdb=" N VAL A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 807 through 829 removed outlier: 3.755A pdb=" N GLN A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 855 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 938 through 946 removed outlier: 3.820A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.933A pdb=" N ARG F 424 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.686A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 467 Processing helix chain 'F' and resid 479 through 489 Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 530 through 541 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 604 through 611 Processing helix chain 'F' and resid 612 through 616 Processing helix chain 'F' and resid 646 through 653 removed outlier: 4.051A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 673 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 704 removed outlier: 3.854A pdb=" N CYS F 704 " --> pdb=" O ILE F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.666A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL F 719 " --> pdb=" O GLN F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 746 removed outlier: 3.842A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 852 through 855 Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 921 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.953A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 426 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.633A pdb=" N ASN E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 490 removed outlier: 4.227A pdb=" N GLU E 488 " --> pdb=" O GLN E 484 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 510 Processing helix chain 'E' and resid 528 through 540 removed outlier: 3.559A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 682 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 807 through 827 Processing helix chain 'E' and resid 852 through 855 Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 895 through 906 Processing helix chain 'E' and resid 913 through 915 No H-bonds generated for 'chain 'E' and resid 913 through 915' Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 925 through 929 removed outlier: 3.598A pdb=" N GLU E 929 " --> pdb=" O PHE E 926 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.868A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 588 through 589 removed outlier: 6.657A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 764 through 771 Processing sheet with id=AA3, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.709A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 548 removed outlier: 7.063A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 689 through 690 Processing sheet with id=AA6, first strand: chain 'B' and resid 764 through 771 Processing sheet with id=AA7, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913 removed outlier: 6.866A pdb=" N ILE B 910 " --> pdb=" O HIS B 934 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL B 936 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 912 " --> pdb=" O VAL B 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AB1, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.581A pdb=" N LYS A 690 " --> pdb=" O VAL A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.398A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N VAL A 764 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N MET A 879 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 766 " --> pdb=" O MET A 879 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 910 " --> pdb=" O HIS A 934 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 936 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 770 through 771 removed outlier: 3.790A pdb=" N GLY A 774 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AB5, first strand: chain 'F' and resid 545 through 548 removed outlier: 6.802A pdb=" N ILE F 587 " --> pdb=" O ILE F 636 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR F 638 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE F 589 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.533A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 764 through 766 removed outlier: 6.203A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 769 through 771 Processing sheet with id=AB9, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.638A pdb=" N ILE F 910 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F 936 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU F 912 " --> pdb=" O VAL F 936 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 882 through 883 Processing sheet with id=AC2, first strand: chain 'E' and resid 546 through 548 removed outlier: 6.248A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.786A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 765 through 771 removed outlier: 6.114A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 877 through 879 884 hydrogen bonds defined for protein. 2577 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: 2.55 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6077 1.34 - 1.46: 3026 1.46 - 1.57: 9370 1.57 - 1.69: 15 1.69 - 1.81: 139 Bond restraints: 18627 Sorted by residual: bond pdb=" C VAL E 911 " pdb=" N LEU E 912 " ideal model delta sigma weight residual 1.331 1.252 0.079 1.59e-02 3.96e+03 2.46e+01 bond pdb=" C ILE B 889 " pdb=" N LEU B 890 " ideal model delta sigma weight residual 1.331 1.229 0.102 2.07e-02 2.33e+03 2.44e+01 bond pdb=" CA ASP A 643 " pdb=" C ASP A 643 " ideal model delta sigma weight residual 1.523 1.492 0.032 1.34e-02 5.57e+03 5.59e+00 bond pdb=" CA LYS C 918 " pdb=" C LYS C 918 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.22e+00 bond pdb=" C4 ADP B1000 " pdb=" C5 ADP B1000 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 18622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 24548 1.83 - 3.65: 721 3.65 - 5.48: 120 5.48 - 7.30: 26 7.30 - 9.13: 5 Bond angle restraints: 25420 Sorted by residual: angle pdb=" N VAL B 555 " pdb=" CA VAL B 555 " pdb=" C VAL B 555 " ideal model delta sigma weight residual 112.80 106.85 5.95 1.15e+00 7.56e-01 2.68e+01 angle pdb=" N GLN B 875 " pdb=" CA GLN B 875 " pdb=" C GLN B 875 " ideal model delta sigma weight residual 110.97 115.36 -4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" N GLY A 571 " pdb=" CA GLY A 571 " pdb=" C GLY A 571 " ideal model delta sigma weight residual 113.18 121.46 -8.28 2.37e+00 1.78e-01 1.22e+01 angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 112.04 107.25 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" C GLU A 557 " pdb=" N ILE A 558 " pdb=" CA ILE A 558 " ideal model delta sigma weight residual 123.08 119.82 3.26 1.01e+00 9.80e-01 1.04e+01 ... (remaining 25415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 10646 24.36 - 48.72: 460 48.72 - 73.08: 33 73.08 - 97.44: 21 97.44 - 121.80: 2 Dihedral angle restraints: 11162 sinusoidal: 3808 harmonic: 7354 Sorted by residual: dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual 300.00 178.20 121.80 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C5' ADP A1000 " pdb=" O5' ADP A1000 " pdb=" PA ADP A1000 " pdb=" O2A ADP A1000 " ideal model delta sinusoidal sigma weight residual -60.00 -165.05 105.05 1 2.00e+01 2.50e-03 3.02e+01 dihedral pdb=" CA ARG C 874 " pdb=" C ARG C 874 " pdb=" N GLN C 875 " pdb=" CA GLN C 875 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 11159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1674 0.033 - 0.066: 937 0.066 - 0.100: 332 0.100 - 0.133: 117 0.133 - 0.166: 15 Chirality restraints: 3075 Sorted by residual: chirality pdb=" CA PRO A 762 " pdb=" N PRO A 762 " pdb=" C PRO A 762 " pdb=" CB PRO A 762 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C4' ADP B1000 " pdb=" C3' ADP B1000 " pdb=" C5' ADP B1000 " pdb=" O4' ADP B1000 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE E 636 " pdb=" CA ILE E 636 " pdb=" CG1 ILE E 636 " pdb=" CG2 ILE E 636 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 3072 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 584 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO F 585 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 585 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 585 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 572 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C LYS A 572 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A 572 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 573 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 849 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO F 850 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 850 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 850 " -0.030 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 418 2.69 - 3.24: 18750 3.24 - 3.79: 28391 3.79 - 4.35: 36461 4.35 - 4.90: 60258 Nonbonded interactions: 144278 Sorted by model distance: nonbonded pdb=" OG1 THR B 886 " pdb=" OH TYR A 757 " model vdw 2.133 3.040 nonbonded pdb=" O VAL E 527 " pdb=" OH TYR E 661 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU A 671 " pdb=" OG SER A 693 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR E 771 " pdb=" O GLY E 774 " model vdw 2.183 3.040 nonbonded pdb=" O VAL C 527 " pdb=" OH TYR C 661 " model vdw 2.195 3.040 ... (remaining 144273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N o \ r name CA or name C or name O or name CB )) or resid 446 or (resid 447 through 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 or (res \ id 470 and (name N or name CA or name C or name O or name CB )) or (resid 471 th \ rough 473 and (name N or name CA or name C or name O or name CB )) or resid 474 \ or (resid 475 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 493 or (resid 494 through 49 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or re \ sid 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) o \ r resid 502 through 503 or (resid 504 through 506 and (name N or name CA or name \ C or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 an \ d (name N or name CA or name C or name O or name CB )) or resid 512 or resid 520 \ through 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 533 or (resid 534 and (name N or name CA or name C or n \ ame O or name CB )) or resid 535 or (resid 536 through 537 and (name N or name C \ A or name C or name O or name CB )) or resid 538 through 539 or (resid 540 throu \ gh 544 and (name N or name CA or name C or name O or name CB )) or resid 545 or \ (resid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 \ through 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or (resid 554 through 558 and (name N or name CA or name C or name O or name \ CB )) or (resid 571 through 575 and (name N or name CA or name C or name O or n \ ame CB )) or resid 576 or (resid 577 through 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 585 or (resid 586 through 588 and \ (name N or name CA or name C or name O or name CB )) or resid 589 through 590 o \ r (resid 591 through 612 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 618 through 626 and (name N or name CA or name C or name O or name C \ B )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or \ name O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name \ CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 639 or (resid 640 \ and (name N or name CA or name C or name O or name CB )) or resid 641 through 64 \ 3 or (resid 644 and (name N or name CA or name C or name O or name CB )) or resi \ d 645 through 646 or (resid 647 and (name N or name CA or name C or name O or na \ me CB )) or resid 648 through 649 or (resid 650 through 652 and (name N or name \ CA or name C or name O or name CB )) or resid 653 or (resid 654 through 655 and \ (name N or name CA or name C or name O or name CB )) or resid 656 through 664 or \ (resid 665 through 666 and (name N or name CA or name C or name O or name CB )) \ or resid 667 through 668 or (resid 669 through 673 and (name N or name CA or na \ me C or name O or name CB )) or resid 674 through 676 or (resid 677 through 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 3 or (resid 684 through 686 and (name N or name CA or name C or name O or name C \ B )) or resid 687 or resid 692 through 694 or (resid 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 through 702 or (resid 703 and (na \ me N or name CA or name C or name O or name CB )) or resid 704 or (resid 705 thr \ ough 706 and (name N or name CA or name C or name O or name CB )) or resid 707 t \ hrough 709 or (resid 710 and (name N or name CA or name C or name O or name CB ) \ ) or resid 711 through 721 or (resid 722 and (name N or name CA or name C or nam \ e O or name CB )) or resid 723 through 725 or (resid 726 and (name N or name CA \ or name C or name O or name CB )) or resid 727 through 731 or (resid 741 and (na \ me N or name CA or name C or name O or name CB )) or resid 742 or (resid 743 thr \ ough 744 and (name N or name CA or name C or name O or name CB )) or resid 745 t \ hrough 747 or (resid 748 and (name N or name CA or name C or name O or name CB ) \ ) or resid 749 through 751 or (resid 752 through 755 and (name N or name CA or n \ ame C or name O or name CB )) or resid 756 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 786 or (resid \ 787 through 791 and (name N or name CA or name C or name O or name CB )) or res \ id 798 through 800 or (resid 801 and (name N or name CA or name C or name O or n \ ame CB )) or resid 802 through 804 or (resid 805 and (name N or name CA or name \ C or name O or name CB )) or resid 806 through 821 or (resid 822 through 823 and \ (name N or name CA or name C or name O or name CB )) or resid 824 through 825 o \ r (resid 826 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 27 through 832 or (resid 833 and (name N or name CA or name C or name O or name \ CB )) or resid 834 through 836 or (resid 837 and (name N or name CA or name C or \ name O or name CB )) or resid 838 through 850 or (resid 851 and (name N or name \ CA or name C or name O or name CB )) or resid 852 through 870 or (resid 871 and \ (name N or name CA or name C or name O or name CB )) or resid 872 through 874 o \ r (resid 875 through 876 and (name N or name CA or name C or name O or name CB ) \ ) or resid 877 through 884 or (resid 885 through 886 and (name N or name CA or n \ ame C or name O or name CB )) or resid 887 or (resid 888 and (name N or name CA \ or name C or name O or name CB )) or resid 889 through 895 or (resid 896 and (na \ me N or name CA or name C or name O or name CB )) or resid 897 or (resid 898 and \ (name N or name CA or name C or name O or name CB )) or resid 899 through 916 o \ r (resid 917 through 918 and (name N or name CA or name C or name O or name CB ) \ ) or resid 919 through 921 or (resid 922 and (name N or name CA or name C or nam \ e O or name CB )) or resid 923 through 928 or (resid 929 and (name N or name CA \ or name C or name O or name CB )) or resid 930 through 936 or (resid 937 through \ 938 and (name N or name CA or name C or name O or name CB )) or resid 939 throu \ gh 1000)) selection = (chain 'B' and (resid 421 through 432 or (resid 433 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 446 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 or (resid 470 and (name \ N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 throu \ gh 473 and (name N or name CA or name C or name O or name CB )) or resid 474 or \ (resid 475 through 483 and (name N or name CA or name C or name O or name CB )) \ or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or nam \ e C or name O or name CB )) or resid 491 through 493 or (resid 494 through 496 a \ nd (name N or name CA or name C or name O or name CB )) or resid 497 through 498 \ or (resid 499 and (name N or name CA or name C or name O or name CB )) or resid \ 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or r \ esid 502 through 503 or (resid 504 through 506 and (name N or name CA or name C \ or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 and ( \ name N or name CA or name C or name O or name CB )) or resid 512 or resid 520 th \ rough 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) \ or resid 523 through 533 or (resid 534 and (name N or name CA or name C or name \ O or name CB )) or resid 535 or (resid 536 through 537 and (name N or name CA o \ r name C or name O or name CB )) or resid 538 through 539 or (resid 540 through \ 544 and (name N or name CA or name C or name O or name CB )) or resid 545 throug \ h 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ (resid 554 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 571 or (resid 572 through 575 and (name N or name CA or name C or name \ O or name CB )) or resid 576 or (resid 577 through 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 through 5 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 589 through \ 591 or (resid 592 through 612 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 618 through 626 and (name N or name CA or name C or name O or \ name CB )) or resid 627 or (resid 628 through 629 and (name N or name CA or name \ C or name O or name CB )) or resid 630 through 631 or (resid 632 and (name N or \ name CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB )) or resid 635 through 639 or (resi \ d 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 646 or (resid 647 and (name N or name CA or name C or name O or name CB )) o \ r resid 648 through 650 or (resid 651 through 652 and (name N or name CA or name \ C or name O or name CB )) or resid 653 or (resid 654 through 655 and (name N or \ name CA or name C or name O or name CB )) or resid 656 through 665 or (resid 66 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 667 through \ 668 or (resid 669 through 673 and (name N or name CA or name C or name O or name \ CB )) or resid 674 through 676 or (resid 677 through 678 and (name N or name CA \ or name C or name O or name CB )) or resid 679 through 683 or (resid 684 throug \ h 686 and (name N or name CA or name C or name O or name CB )) or resid 687 or r \ esid 692 through 694 or (resid 695 and (name N or name CA or name C or name O or \ name CB )) or resid 696 through 702 or (resid 703 and (name N or name CA or nam \ e C or name O or name CB )) or resid 704 or (resid 705 through 706 and (name N o \ r name CA or name C or name O or name CB )) or resid 707 through 709 or (resid 7 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 711 through \ 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) or r \ esid 718 through 721 or (resid 722 and (name N or name CA or name C or name O or \ name CB )) or resid 723 through 730 or (resid 731 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 741 and (name N or name CA or name C or na \ me O or name CB )) or resid 742 or (resid 743 through 744 and (name N or name CA \ or name C or name O or name CB )) or resid 745 through 747 or (resid 748 and (n \ ame N or name CA or name C or name O or name CB )) or resid 749 through 751 or ( \ resid 752 through 755 and (name N or name CA or name C or name O or name CB )) o \ r resid 756 through 772 or (resid 773 and (name N or name CA or name C or name O \ or name CB )) or resid 774 through 786 or (resid 787 through 791 and (name N or \ name CA or name C or name O or name CB )) or resid 798 through 804 or (resid 80 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 806 through \ 825 or (resid 826 and (name N or name CA or name C or name O or name CB )) or re \ sid 827 through 832 or (resid 833 and (name N or name CA or name C or name O or \ name CB )) or resid 834 through 836 or (resid 837 and (name N or name CA or name \ C or name O or name CB )) or resid 838 through 850 or (resid 851 and (name N or \ name CA or name C or name O or name CB )) or resid 852 through 870 or (resid 87 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 872 through \ 874 or (resid 875 through 876 and (name N or name CA or name C or name O or name \ CB )) or resid 877 through 884 or (resid 885 through 886 and (name N or name CA \ or name C or name O or name CB )) or resid 887 or (resid 888 and (name N or nam \ e CA or name C or name O or name CB )) or resid 889 through 895 or (resid 896 an \ d (name N or name CA or name C or name O or name CB )) or resid 897 or (resid 89 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 899 through \ 921 or (resid 922 and (name N or name CA or name C or name O or name CB )) or re \ sid 923 through 937 or (resid 938 and (name N or name CA or name C or name O or \ name CB )) or resid 939 through 1000)) selection = (chain 'C' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 462 or (resid 463 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 474 or (resid 4 \ 75 through 483 and (name N or name CA or name C or name O or name CB )) or resid \ 484 through 488 or (resid 489 through 490 and (name N or name CA or name C or n \ ame O or name CB )) or resid 491 through 493 or (resid 494 through 496 and (name \ N or name CA or name C or name O or name CB )) or resid 497 through 498 or (res \ id 499 and (name N or name CA or name C or name O or name CB )) or resid 500 or \ (resid 501 and (name N or name CA or name C or name O or name CB )) or resid 502 \ through 504 or (resid 505 through 506 and (name N or name CA or name C or name \ O or name CB )) or resid 507 through 508 or (resid 509 through 511 and (name N o \ r name CA or name C or name O or name CB )) or resid 512 or resid 520 through 53 \ 3 or (resid 534 and (name N or name CA or name C or name O or name CB )) or resi \ d 535 through 540 or (resid 541 through 544 and (name N or name CA or name C or \ name O or name CB )) or resid 545 through 548 or (resid 549 and (name N or name \ CA or name C or name O or name CB )) or (resid 554 through 558 and (name N or na \ me CA or name C or name O or name CB )) or (resid 571 through 575 and (name N or \ name CA or name C or name O or name CB )) or resid 576 or (resid 577 through 58 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 585 or (resid 586 through 588 and (name N or name CA or name C or name O or name \ CB )) or resid 589 through 591 or (resid 592 through 612 and (name N or name CA \ or name C or name O or name CB )) or (resid 618 through 626 and (name N or name \ CA or name C or name O or name CB )) or resid 627 through 643 or (resid 644 and \ (name N or name CA or name C or name O or name CB )) or resid 645 through 671 o \ r (resid 672 through 673 and (name N or name CA or name C or name O or name CB ) \ ) or resid 674 through 694 or (resid 695 and (name N or name CA or name C or nam \ e O or name CB )) or resid 696 through 800 or (resid 801 and (name N or name CA \ or name C or name O or name CB )) or resid 802 through 821 or (resid 822 through \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throu \ gh 825 or (resid 826 and (name N or name CA or name C or name O or name CB )) or \ resid 827 through 832 or (resid 833 and (name N or name CA or name C or name O \ or name CB )) or resid 834 through 870 or (resid 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 872 through 874 or (resid 875 through 876 \ and (name N or name CA or name C or name O or name CB )) or resid 877 through 8 \ 84 or (resid 885 through 886 and (name N or name CA or name C or name O or name \ CB )) or resid 887 through 897 or (resid 898 and (name N or name CA or name C or \ name O or name CB )) or resid 899 through 928 or (resid 929 and (name N or name \ CA or name C or name O or name CB )) or resid 930 through 937 or (resid 938 and \ (name N or name CA or name C or name O or name CB )) or resid 939 or (resid 940 \ and (name N or name CA or name C or name O or name CB )) or resid 941 through 1 \ 000)) selection = (chain 'E' and (resid 421 through 433 or (resid 434 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 446 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 472 or (resid 4 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 474 through \ 494 or (resid 495 through 496 and (name N or name CA or name C or name O or nam \ e CB )) or resid 497 through 502 or (resid 503 through 506 and (name N or name C \ A or name C or name O or name CB )) or resid 507 through 521 or (resid 522 and ( \ name N or name CA or name C or name O or name CB )) or resid 523 through 535 or \ (resid 536 through 537 and (name N or name CA or name C or name O or name CB )) \ or resid 538 through 558 or resid 571 through 581 or (resid 582 through 583 and \ (name N or name CA or name C or name O or name CB )) or resid 584 through 589 or \ (resid 590 through 595 and (name N or name CA or name C or name O or name CB )) \ or (resid 603 through 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or n \ ame O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name C \ A or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or na \ me CA or name C or name O or name CB )) or resid 635 through 639 or (resid 640 a \ nd (name N or name CA or name C or name O or name CB )) or resid 641 through 642 \ or (resid 643 through 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 653 or (resid 654 through 655 and (name N or name CA or \ name C or name O or name CB )) or resid 656 through 664 or (resid 665 through 6 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 667 through \ 668 or (resid 669 through 673 and (name N or name CA or name C or name O or nam \ e CB )) or resid 674 through 676 or (resid 677 through 678 and (name N or name C \ A or name C or name O or name CB )) or resid 679 through 683 or (resid 684 throu \ gh 686 and (name N or name CA or name C or name O or name CB )) or resid 687 or \ resid 692 through 702 or (resid 703 and (name N or name CA or name C or name O o \ r name CB )) or resid 704 or (resid 705 through 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 709 or (resid 710 and (name N \ or name CA or name C or name O or name CB )) or resid 711 through 716 or (resid \ 717 and (name N or name CA or name C or name O or name CB )) or resid 718 throug \ h 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 725 or (resid 726 and (name N or name CA or name C or name O o \ r name CB )) or resid 727 through 730 or (resid 731 and (name N or name CA or na \ me C or name O or name CB )) or (resid 741 and (name N or name CA or name C or n \ ame O or name CB )) or resid 742 through 743 or (resid 744 and (name N or name C \ A or name C or name O or name CB )) or resid 745 through 747 or (resid 748 and ( \ name N or name CA or name C or name O or name CB )) or resid 749 through 751 or \ (resid 752 through 755 and (name N or name CA or name C or name O or name CB )) \ or resid 756 through 772 or (resid 773 and (name N or name CA or name C or name \ O or name CB )) or resid 774 through 786 or (resid 787 through 795 and (name N o \ r name CA or name C or name O or name CB )) or resid 798 through 800 or (resid 8 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 802 through \ 804 or (resid 805 and (name N or name CA or name C or name O or name CB )) or r \ esid 806 through 845 or (resid 846 and (name N or name CA or name C or name O or \ name CB )) or resid 847 through 850 or (resid 851 and (name N or name CA or nam \ e C or name O or name CB )) or resid 852 through 874 or (resid 875 through 876 a \ nd (name N or name CA or name C or name O or name CB )) or resid 877 through 885 \ or (resid 886 and (name N or name CA or name C or name O or name CB )) or resid \ 887 through 895 or (resid 896 and (name N or name CA or name C or name O or nam \ e CB )) or resid 897 through 921 or (resid 922 and (name N or name CA or name C \ or name O or name CB )) or resid 923 through 1000)) selection = (chain 'F' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 or (resid 432 through 445 and (name N or name CA or \ name C or name O or name CB )) or resid 446 or (resid 447 through 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 or (resid 470 and ( \ name N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 t \ hrough 473 and (name N or name CA or name C or name O or name CB )) or resid 474 \ or (resid 475 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 493 or (resid 494 through 4 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 503 or (resid 504 through 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 a \ nd (name N or name CA or name C or name O or name CB )) or resid 512 or resid 52 \ 0 through 521 or (resid 522 and (name N or name CA or name C or name O or name C \ B )) or resid 523 through 535 or (resid 536 through 537 and (name N or name CA o \ r name C or name O or name CB )) or resid 538 through 539 or (resid 540 through \ 544 and (name N or name CA or name C or name O or name CB )) or resid 545 or (re \ sid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 th \ rough 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) \ or (resid 554 through 558 and (name N or name CA or name C or name O or name CB \ )) or resid 571 or (resid 572 through 575 and (name N or name CA or name C or n \ ame O or name CB )) or resid 576 or (resid 577 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 throu \ gh 588 and (name N or name CA or name C or name O or name CB )) or resid 589 or \ (resid 590 through 612 and (name N or name CA or name C or name O or name CB )) \ or (resid 618 through 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or na \ me O or name CB )) or resid 630 through 633 or (resid 634 and (name N or name CA \ or name C or name O or name CB )) or resid 635 through 639 or (resid 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 642 or ( \ resid 643 through 644 and (name N or name CA or name C or name O or name CB )) o \ r resid 645 through 646 or (resid 647 and (name N or name CA or name C or name O \ or name CB )) or resid 648 through 650 or (resid 651 through 652 and (name N or \ name CA or name C or name O or name CB )) or resid 653 or (resid 654 through 65 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 656 through \ 664 or (resid 665 through 666 and (name N or name CA or name C or name O or name \ CB )) or resid 667 through 668 or (resid 669 through 673 and (name N or name CA \ or name C or name O or name CB )) or resid 674 through 676 or (resid 677 throug \ h 678 and (name N or name CA or name C or name O or name CB )) or resid 679 thro \ ugh 683 or (resid 684 through 686 and (name N or name CA or name C or name O or \ name CB )) or resid 687 or resid 692 through 694 or (resid 695 and (name N or na \ me CA or name C or name O or name CB )) or resid 696 through 702 or (resid 703 a \ nd (name N or name CA or name C or name O or name CB )) or resid 704 or (resid 7 \ 05 through 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 709 or (resid 710 and (name N or name CA or name C or name O or nam \ e CB )) or resid 711 through 716 or (resid 717 and (name N or name CA or name C \ or name O or name CB )) or resid 718 through 721 or (resid 722 and (name N or na \ me CA or name C or name O or name CB )) or resid 723 through 725 or (resid 726 a \ nd (name N or name CA or name C or name O or name CB )) or resid 727 through 730 \ or (resid 731 and (name N or name CA or name C or name O or name CB )) or (resi \ d 741 and (name N or name CA or name C or name O or name CB )) or resid 742 or ( \ resid 743 through 744 and (name N or name CA or name C or name O or name CB )) o \ r resid 745 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 751 or (resid 752 through 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 772 or (resid 77 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 786 or (resid 787 through 791 and (name N or name CA or name C or name O or name \ CB )) or resid 798 through 800 or (resid 801 and (name N or name CA or name C o \ r name O or name CB )) or resid 802 through 804 or (resid 805 and (name N or nam \ e CA or name C or name O or name CB )) or resid 806 through 825 or (resid 826 an \ d (name N or name CA or name C or name O or name CB )) or resid 827 through 836 \ or (resid 837 and (name N or name CA or name C or name O or name CB )) or resid \ 838 through 850 or (resid 851 and (name N or name CA or name C or name O or name \ CB )) or resid 852 through 870 or (resid 871 and (name N or name CA or name C o \ r name O or name CB )) or resid 872 through 875 or (resid 876 and (name N or nam \ e CA or name C or name O or name CB )) or resid 877 through 884 or (resid 885 th \ rough 886 and (name N or name CA or name C or name O or name CB )) or resid 887 \ or (resid 888 and (name N or name CA or name C or name O or name CB )) or resid \ 889 through 895 or (resid 896 and (name N or name CA or name C or name O or name \ CB )) or resid 897 or (resid 898 and (name N or name CA or name C or name O or \ name CB )) or resid 899 through 914 or (resid 915 and (name N or name CA or name \ C or name O or name CB )) or resid 916 or (resid 917 through 918 and (name N or \ name CA or name C or name O or name CB )) or resid 919 through 921 or (resid 92 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 923 through \ 936 or (resid 937 through 938 and (name N or name CA or name C or name O or name \ CB )) or resid 939 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.007 0.102 18627 Z= 0.306 Angle : 0.776 9.130 25420 Z= 0.417 Chirality : 0.047 0.166 3075 Planarity : 0.005 0.057 3261 Dihedral : 14.074 121.800 6408 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.12 % Allowed : 9.62 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.14), residues: 2515 helix: -1.77 (0.13), residues: 1125 sheet: -2.30 (0.25), residues: 322 loop : -2.89 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 786 TYR 0.022 0.003 TYR A 939 PHE 0.020 0.002 PHE A 820 TRP 0.015 0.002 TRP B 470 HIS 0.008 0.002 HIS F 841 Details of bonding type rmsd covalent geometry : bond 0.00717 (18627) covalent geometry : angle 0.77585 (25420) hydrogen bonds : bond 0.09124 ( 884) hydrogen bonds : angle 5.65229 ( 2577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 517 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7153 (mtmt) REVERT: C 715 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6695 (mm-40) REVERT: C 720 LEU cc_start: 0.7647 (tt) cc_final: 0.7336 (tt) REVERT: B 647 GLU cc_start: 0.7835 (tp30) cc_final: 0.7569 (tp30) REVERT: F 435 MET cc_start: 0.7690 (mmm) cc_final: 0.7482 (tpp) REVERT: F 461 TYR cc_start: 0.5914 (t80) cc_final: 0.4941 (m-10) REVERT: F 543 GLU cc_start: 0.8135 (mp0) cc_final: 0.7613 (mp0) REVERT: F 612 ASP cc_start: 0.6467 (m-30) cc_final: 0.6024 (m-30) REVERT: E 810 MET cc_start: 0.8147 (tpt) cc_final: 0.7850 (tpp) REVERT: E 934 HIS cc_start: 0.7876 (m170) cc_final: 0.7508 (m170) outliers start: 2 outliers final: 1 residues processed: 250 average time/residue: 0.1355 time to fit residues: 51.6240 Evaluate side-chains 189 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 802 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS C 843 HIS B 715 GLN B 743 GLN A 561 HIS A 622 HIS A 839 HIS A 841 HIS A 876 ASN F 477 ASN F 575 GLN F 677 GLN F 702 GLN E 677 GLN E 916 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098374 restraints weight = 34958.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095889 restraints weight = 42981.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096940 restraints weight = 36540.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097326 restraints weight = 23497.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097659 restraints weight = 21366.990| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18627 Z= 0.144 Angle : 0.624 8.340 25420 Z= 0.305 Chirality : 0.042 0.161 3075 Planarity : 0.005 0.053 3261 Dihedral : 7.416 110.015 2753 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.98 % Allowed : 13.59 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.16), residues: 2515 helix: 0.00 (0.15), residues: 1139 sheet: -1.59 (0.26), residues: 330 loop : -2.21 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 815 TYR 0.016 0.002 TYR C 544 PHE 0.014 0.001 PHE C 820 TRP 0.012 0.001 TRP B 470 HIS 0.005 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00342 (18627) covalent geometry : angle 0.62410 (25420) hydrogen bonds : bond 0.03257 ( 884) hydrogen bonds : angle 4.70522 ( 2577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 552 MET cc_start: 0.6160 (ptm) cc_final: 0.5630 (ttp) REVERT: F 430 VAL cc_start: 0.7970 (m) cc_final: 0.7613 (m) REVERT: F 461 TYR cc_start: 0.6052 (t80) cc_final: 0.5223 (m-10) REVERT: F 612 ASP cc_start: 0.6743 (m-30) cc_final: 0.6520 (m-30) REVERT: E 655 MET cc_start: 0.6102 (mmp) cc_final: 0.5762 (mmp) REVERT: E 810 MET cc_start: 0.8024 (tpt) cc_final: 0.7556 (tpp) REVERT: E 869 MET cc_start: 0.6862 (mtp) cc_final: 0.6651 (mtp) REVERT: E 882 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: E 934 HIS cc_start: 0.7759 (m170) cc_final: 0.7305 (m170) outliers start: 34 outliers final: 21 residues processed: 240 average time/residue: 0.1098 time to fit residues: 42.0459 Evaluate side-chains 209 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 882 GLU Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 54 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 50.0000 chunk 251 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN F 561 HIS F 615 GLN E 484 GLN E 640 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.123843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097351 restraints weight = 35326.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094720 restraints weight = 44236.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095558 restraints weight = 39444.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096180 restraints weight = 24628.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096592 restraints weight = 21576.653| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18627 Z= 0.187 Angle : 0.635 7.892 25420 Z= 0.310 Chirality : 0.043 0.162 3075 Planarity : 0.005 0.049 3261 Dihedral : 7.303 106.564 2753 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.32 % Allowed : 15.28 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.16), residues: 2515 helix: 0.52 (0.16), residues: 1132 sheet: -1.28 (0.27), residues: 321 loop : -1.95 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 538 TYR 0.019 0.002 TYR A 939 PHE 0.017 0.002 PHE A 820 TRP 0.009 0.001 TRP B 470 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00455 (18627) covalent geometry : angle 0.63479 (25420) hydrogen bonds : bond 0.03403 ( 884) hydrogen bonds : angle 4.59293 ( 2577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6266 (ptm) cc_final: 0.5761 (ttp) REVERT: C 757 TYR cc_start: 0.6580 (m-10) cc_final: 0.6171 (m-10) REVERT: F 461 TYR cc_start: 0.6059 (t80) cc_final: 0.5192 (m-10) REVERT: F 464 TRP cc_start: 0.4411 (m100) cc_final: 0.4042 (m100) REVERT: F 612 ASP cc_start: 0.6757 (m-30) cc_final: 0.6531 (m-30) REVERT: F 619 PHE cc_start: 0.6327 (t80) cc_final: 0.6056 (t80) REVERT: F 840 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9292 (mm) REVERT: E 655 MET cc_start: 0.6049 (mmp) cc_final: 0.5513 (mmp) REVERT: E 810 MET cc_start: 0.8040 (tpt) cc_final: 0.7608 (tpp) REVERT: E 934 HIS cc_start: 0.7759 (m170) cc_final: 0.7266 (m170) outliers start: 57 outliers final: 49 residues processed: 245 average time/residue: 0.1131 time to fit residues: 45.0988 Evaluate side-chains 227 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 179 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 228 optimal weight: 0.0070 chunk 81 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 209 optimal weight: 50.0000 chunk 26 optimal weight: 2.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN F 561 HIS E 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097542 restraints weight = 35244.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093366 restraints weight = 27855.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094672 restraints weight = 32100.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094556 restraints weight = 22234.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094808 restraints weight = 18902.354| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18627 Z= 0.133 Angle : 0.591 8.332 25420 Z= 0.286 Chirality : 0.042 0.147 3075 Planarity : 0.004 0.052 3261 Dihedral : 7.022 100.569 2753 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.27 % Allowed : 17.73 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2515 helix: 0.93 (0.16), residues: 1136 sheet: -1.10 (0.27), residues: 339 loop : -1.70 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 482 TYR 0.015 0.001 TYR A 939 PHE 0.014 0.001 PHE C 820 TRP 0.009 0.001 TRP B 470 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00317 (18627) covalent geometry : angle 0.59117 (25420) hydrogen bonds : bond 0.03020 ( 884) hydrogen bonds : angle 4.36230 ( 2577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6177 (ptm) cc_final: 0.5592 (ttp) REVERT: C 757 TYR cc_start: 0.6775 (m-10) cc_final: 0.6287 (m-10) REVERT: A 591 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6855 (mm-30) REVERT: F 461 TYR cc_start: 0.5627 (t80) cc_final: 0.4760 (m-10) REVERT: F 612 ASP cc_start: 0.6728 (m-30) cc_final: 0.6275 (m-30) REVERT: F 619 PHE cc_start: 0.6501 (t80) cc_final: 0.6121 (t80) REVERT: E 655 MET cc_start: 0.6086 (mmp) cc_final: 0.5598 (mmp) REVERT: E 922 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6977 (p0) REVERT: E 934 HIS cc_start: 0.7732 (m170) cc_final: 0.7350 (m170) outliers start: 56 outliers final: 45 residues processed: 246 average time/residue: 0.1118 time to fit residues: 44.7171 Evaluate side-chains 233 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 199 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN F 561 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097019 restraints weight = 35008.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.093079 restraints weight = 30973.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093990 restraints weight = 32589.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094422 restraints weight = 20794.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094900 restraints weight = 18516.422| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18627 Z= 0.158 Angle : 0.604 9.503 25420 Z= 0.291 Chirality : 0.042 0.150 3075 Planarity : 0.005 0.052 3261 Dihedral : 6.954 94.858 2753 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.37 % Allowed : 17.38 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.17), residues: 2515 helix: 1.06 (0.16), residues: 1135 sheet: -0.82 (0.28), residues: 327 loop : -1.61 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 538 TYR 0.017 0.002 TYR A 939 PHE 0.016 0.001 PHE A 820 TRP 0.007 0.001 TRP B 470 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00382 (18627) covalent geometry : angle 0.60436 (25420) hydrogen bonds : bond 0.03115 ( 884) hydrogen bonds : angle 4.32614 ( 2577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6321 (ptm) cc_final: 0.5840 (ttp) REVERT: C 577 LEU cc_start: 0.6745 (pp) cc_final: 0.6217 (tp) REVERT: C 757 TYR cc_start: 0.6784 (m-10) cc_final: 0.6286 (m-10) REVERT: A 591 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6685 (mm-30) REVERT: F 461 TYR cc_start: 0.6021 (t80) cc_final: 0.5070 (m-10) REVERT: F 612 ASP cc_start: 0.6792 (m-30) cc_final: 0.6436 (m-30) REVERT: F 619 PHE cc_start: 0.6432 (t80) cc_final: 0.6115 (t80) REVERT: F 840 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9288 (mm) REVERT: E 810 MET cc_start: 0.8114 (tpt) cc_final: 0.7839 (tpp) REVERT: E 922 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6972 (p0) REVERT: E 934 HIS cc_start: 0.7781 (m170) cc_final: 0.7360 (m170) outliers start: 75 outliers final: 65 residues processed: 255 average time/residue: 0.1150 time to fit residues: 47.6275 Evaluate side-chains 253 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 877 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 169 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 48 optimal weight: 0.0570 chunk 156 optimal weight: 20.0000 chunk 252 optimal weight: 0.8980 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN F 561 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097854 restraints weight = 34859.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093653 restraints weight = 29155.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094957 restraints weight = 29633.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095262 restraints weight = 19316.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095695 restraints weight = 17628.774| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18627 Z= 0.118 Angle : 0.575 7.757 25420 Z= 0.275 Chirality : 0.041 0.150 3075 Planarity : 0.004 0.049 3261 Dihedral : 6.714 86.219 2753 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.73 % Allowed : 18.25 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2515 helix: 1.30 (0.16), residues: 1136 sheet: -0.83 (0.27), residues: 347 loop : -1.43 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 482 TYR 0.014 0.001 TYR A 939 PHE 0.018 0.001 PHE F 545 TRP 0.008 0.001 TRP F 464 HIS 0.006 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00285 (18627) covalent geometry : angle 0.57500 (25420) hydrogen bonds : bond 0.02829 ( 884) hydrogen bonds : angle 4.17923 ( 2577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6029 (ptm) cc_final: 0.5497 (ttp) REVERT: C 577 LEU cc_start: 0.6635 (pp) cc_final: 0.6169 (tp) REVERT: C 757 TYR cc_start: 0.6768 (m-10) cc_final: 0.6321 (m-10) REVERT: B 464 TRP cc_start: 0.6593 (m100) cc_final: 0.6388 (m100) REVERT: A 557 GLU cc_start: 0.6821 (tt0) cc_final: 0.6386 (tt0) REVERT: A 591 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6637 (mm-30) REVERT: F 461 TYR cc_start: 0.5983 (t80) cc_final: 0.5064 (m-10) REVERT: F 552 MET cc_start: 0.3082 (ppp) cc_final: 0.2591 (ppp) REVERT: F 579 LYS cc_start: 0.8136 (tptm) cc_final: 0.7813 (tppt) REVERT: F 612 ASP cc_start: 0.6720 (m-30) cc_final: 0.6376 (m-30) REVERT: F 619 PHE cc_start: 0.6441 (t80) cc_final: 0.6124 (t80) REVERT: F 840 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9294 (mm) REVERT: E 655 MET cc_start: 0.6199 (mmp) cc_final: 0.5844 (mmp) REVERT: E 922 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6946 (p0) REVERT: E 934 HIS cc_start: 0.7736 (m170) cc_final: 0.7358 (m170) outliers start: 64 outliers final: 55 residues processed: 258 average time/residue: 0.1110 time to fit residues: 46.7367 Evaluate side-chains 248 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 19 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 32 optimal weight: 30.0000 chunk 215 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 136 optimal weight: 0.4980 chunk 49 optimal weight: 8.9990 chunk 206 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN B 677 GLN F 561 HIS E 484 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096568 restraints weight = 35085.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093149 restraints weight = 33374.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094192 restraints weight = 34598.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094260 restraints weight = 21529.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095406 restraints weight = 19037.077| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 18627 Z= 0.197 Angle : 0.630 7.964 25420 Z= 0.306 Chirality : 0.043 0.152 3075 Planarity : 0.005 0.050 3261 Dihedral : 6.853 83.529 2753 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.26 % Allowed : 18.78 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2515 helix: 1.11 (0.16), residues: 1143 sheet: -0.76 (0.28), residues: 340 loop : -1.43 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 482 TYR 0.019 0.002 TYR B 939 PHE 0.019 0.002 PHE A 820 TRP 0.007 0.001 TRP F 464 HIS 0.008 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00478 (18627) covalent geometry : angle 0.62960 (25420) hydrogen bonds : bond 0.03282 ( 884) hydrogen bonds : angle 4.31801 ( 2577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 194 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.6353 (ptm) cc_final: 0.5981 (ttp) REVERT: C 577 LEU cc_start: 0.6535 (pp) cc_final: 0.6072 (tp) REVERT: B 647 GLU cc_start: 0.7840 (tp30) cc_final: 0.7610 (tp30) REVERT: A 591 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6661 (mm-30) REVERT: F 461 TYR cc_start: 0.6157 (t80) cc_final: 0.5232 (m-10) REVERT: F 552 MET cc_start: 0.3271 (ppp) cc_final: 0.2746 (ppp) REVERT: F 612 ASP cc_start: 0.6841 (m-30) cc_final: 0.6512 (m-30) REVERT: F 619 PHE cc_start: 0.6454 (t80) cc_final: 0.6156 (t80) REVERT: F 840 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9246 (mm) REVERT: E 655 MET cc_start: 0.6252 (mmp) cc_final: 0.5844 (mmp) REVERT: E 810 MET cc_start: 0.8112 (tpt) cc_final: 0.7803 (tpp) REVERT: E 934 HIS cc_start: 0.7792 (m170) cc_final: 0.7361 (m170) outliers start: 73 outliers final: 67 residues processed: 257 average time/residue: 0.1183 time to fit residues: 49.2154 Evaluate side-chains 255 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 187 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 169 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN F 561 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099019 restraints weight = 34717.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095331 restraints weight = 28899.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096453 restraints weight = 33107.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096490 restraints weight = 20506.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096725 restraints weight = 17925.505| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18627 Z= 0.106 Angle : 0.567 9.245 25420 Z= 0.270 Chirality : 0.041 0.146 3075 Planarity : 0.004 0.049 3261 Dihedral : 6.434 85.005 2753 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.38 % Allowed : 20.17 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 2515 helix: 1.49 (0.16), residues: 1136 sheet: -0.77 (0.27), residues: 349 loop : -1.24 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 482 TYR 0.012 0.001 TYR A 939 PHE 0.016 0.001 PHE F 545 TRP 0.009 0.001 TRP F 464 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00246 (18627) covalent geometry : angle 0.56687 (25420) hydrogen bonds : bond 0.02670 ( 884) hydrogen bonds : angle 4.06969 ( 2577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: C 552 MET cc_start: 0.5788 (ptm) cc_final: 0.5333 (ttp) REVERT: C 577 LEU cc_start: 0.6430 (pp) cc_final: 0.6115 (tp) REVERT: C 941 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 581 LYS cc_start: 0.8538 (mtmm) cc_final: 0.8263 (mtmm) REVERT: A 591 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6572 (mm-30) REVERT: F 430 VAL cc_start: 0.6388 (t) cc_final: 0.5717 (m) REVERT: F 461 TYR cc_start: 0.5875 (t80) cc_final: 0.5009 (m-10) REVERT: F 543 GLU cc_start: 0.7663 (mp0) cc_final: 0.7332 (mp0) REVERT: F 552 MET cc_start: 0.2831 (ppp) cc_final: 0.2536 (ppp) REVERT: F 612 ASP cc_start: 0.6589 (m-30) cc_final: 0.6262 (m-30) REVERT: F 619 PHE cc_start: 0.6506 (t80) cc_final: 0.6182 (t80) REVERT: F 717 GLU cc_start: 0.7517 (pt0) cc_final: 0.7314 (mt-10) REVERT: E 643 ASP cc_start: 0.6622 (m-30) cc_final: 0.5946 (m-30) REVERT: E 655 MET cc_start: 0.6214 (mmp) cc_final: 0.5859 (mmp) REVERT: E 810 MET cc_start: 0.8141 (tpt) cc_final: 0.7882 (tpp) REVERT: E 922 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.6985 (p0) REVERT: E 934 HIS cc_start: 0.7748 (m170) cc_final: 0.7340 (m170) outliers start: 58 outliers final: 53 residues processed: 252 average time/residue: 0.1222 time to fit residues: 49.4437 Evaluate side-chains 249 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 766 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 225 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 228 optimal weight: 0.0020 chunk 201 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 221 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 overall best weight: 3.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN F 561 HIS E 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097738 restraints weight = 34901.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.093672 restraints weight = 27285.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094955 restraints weight = 32869.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094859 restraints weight = 20828.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.095502 restraints weight = 18195.583| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18627 Z= 0.147 Angle : 0.594 9.606 25420 Z= 0.284 Chirality : 0.042 0.146 3075 Planarity : 0.004 0.048 3261 Dihedral : 6.432 84.188 2753 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.67 % Allowed : 19.83 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2515 helix: 1.43 (0.16), residues: 1137 sheet: -0.73 (0.27), residues: 350 loop : -1.20 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 482 TYR 0.016 0.002 TYR A 939 PHE 0.016 0.001 PHE A 820 TRP 0.007 0.001 TRP F 464 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00357 (18627) covalent geometry : angle 0.59387 (25420) hydrogen bonds : bond 0.02942 ( 884) hydrogen bonds : angle 4.11486 ( 2577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 552 MET cc_start: 0.5791 (ptm) cc_final: 0.5399 (ttp) REVERT: C 577 LEU cc_start: 0.6563 (pp) cc_final: 0.6349 (tp) REVERT: C 757 TYR cc_start: 0.6891 (m-80) cc_final: 0.6359 (m-10) REVERT: B 581 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8315 (mtmm) REVERT: A 591 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6581 (mm-30) REVERT: F 461 TYR cc_start: 0.5762 (t80) cc_final: 0.4910 (m-10) REVERT: F 543 GLU cc_start: 0.7746 (mp0) cc_final: 0.7399 (mp0) REVERT: F 561 HIS cc_start: 0.6265 (m170) cc_final: 0.6033 (m-70) REVERT: F 612 ASP cc_start: 0.6761 (m-30) cc_final: 0.6367 (m-30) REVERT: F 619 PHE cc_start: 0.6574 (t80) cc_final: 0.6223 (t80) REVERT: F 717 GLU cc_start: 0.7533 (pt0) cc_final: 0.7324 (mt-10) REVERT: E 655 MET cc_start: 0.6235 (mmp) cc_final: 0.5943 (mmp) REVERT: E 810 MET cc_start: 0.8127 (tpt) cc_final: 0.7860 (tpt) REVERT: E 922 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7003 (p0) REVERT: E 934 HIS cc_start: 0.7713 (m170) cc_final: 0.7334 (m170) outliers start: 63 outliers final: 59 residues processed: 248 average time/residue: 0.1127 time to fit residues: 45.1399 Evaluate side-chains 251 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 208 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 114 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN E 875 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097041 restraints weight = 34947.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093276 restraints weight = 31342.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094230 restraints weight = 28824.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094348 restraints weight = 20445.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094776 restraints weight = 19213.834| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18627 Z= 0.155 Angle : 0.607 9.380 25420 Z= 0.291 Chirality : 0.042 0.146 3075 Planarity : 0.004 0.046 3261 Dihedral : 6.473 84.382 2753 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.85 % Allowed : 19.71 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2515 helix: 1.45 (0.16), residues: 1131 sheet: -0.73 (0.27), residues: 350 loop : -1.17 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 482 TYR 0.017 0.002 TYR C 757 PHE 0.016 0.001 PHE A 820 TRP 0.007 0.001 TRP F 464 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00378 (18627) covalent geometry : angle 0.60660 (25420) hydrogen bonds : bond 0.02995 ( 884) hydrogen bonds : angle 4.16480 ( 2577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 196 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 552 MET cc_start: 0.5833 (ptm) cc_final: 0.5441 (ttp) REVERT: C 577 LEU cc_start: 0.6549 (pp) cc_final: 0.6342 (tp) REVERT: C 711 ASN cc_start: 0.7217 (p0) cc_final: 0.6726 (p0) REVERT: B 581 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8314 (mtmm) REVERT: A 591 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6563 (mm-30) REVERT: F 461 TYR cc_start: 0.5837 (t80) cc_final: 0.4983 (m-10) REVERT: F 543 GLU cc_start: 0.7733 (mp0) cc_final: 0.7378 (mp0) REVERT: F 612 ASP cc_start: 0.6765 (m-30) cc_final: 0.6376 (m-30) REVERT: F 619 PHE cc_start: 0.6552 (t80) cc_final: 0.6211 (t80) REVERT: F 717 GLU cc_start: 0.7525 (pt0) cc_final: 0.7303 (mt-10) REVERT: E 810 MET cc_start: 0.8161 (tpt) cc_final: 0.7895 (tpt) REVERT: E 922 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7000 (p0) REVERT: E 934 HIS cc_start: 0.7726 (m170) cc_final: 0.7356 (m170) outliers start: 66 outliers final: 62 residues processed: 249 average time/residue: 0.1119 time to fit residues: 45.0189 Evaluate side-chains 252 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 941 GLU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLN Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 836 VAL Chi-restraints excluded: chain F residue 933 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 658 VAL Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 802 VAL Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 933 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 20 optimal weight: 0.0070 chunk 204 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN E 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098368 restraints weight = 35051.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096531 restraints weight = 42992.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097477 restraints weight = 41507.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097731 restraints weight = 25213.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098765 restraints weight = 22089.782| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18627 Z= 0.162 Angle : 0.610 9.044 25420 Z= 0.293 Chirality : 0.042 0.152 3075 Planarity : 0.004 0.046 3261 Dihedral : 6.492 84.074 2753 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.79 % Allowed : 19.94 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2515 helix: 1.43 (0.16), residues: 1131 sheet: -0.73 (0.27), residues: 350 loop : -1.19 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 482 TYR 0.017 0.002 TYR A 939 PHE 0.017 0.001 PHE A 820 TRP 0.006 0.001 TRP F 464 HIS 0.007 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00394 (18627) covalent geometry : angle 0.61032 (25420) hydrogen bonds : bond 0.03033 ( 884) hydrogen bonds : angle 4.16868 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.06 seconds wall clock time: 45 minutes 15.27 seconds (2715.27 seconds total)