Starting phenix.real_space_refine on Mon Aug 25 01:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ksm_23020/08_2025/7ksm_23020.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ksm_23020/08_2025/7ksm_23020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ksm_23020/08_2025/7ksm_23020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ksm_23020/08_2025/7ksm_23020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ksm_23020/08_2025/7ksm_23020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ksm_23020/08_2025/7ksm_23020.map" } resolution = 3.2 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= 0.050 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 120 5.16 5 C 15541 2.51 5 N 4205 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 219 residue(s): 0.02s 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: 24547 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4009 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4041 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4085 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4098 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "E" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4073 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3999 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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} Time building chain proxies: 5.76, per 1000 atoms: 0.23 Number of scatterers: 24547 At special positions: 0 Unit cell: (127.65, 138, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 16 15.00 Mg 4 11.99 O 4661 8.00 N 4205 7.00 C 15541 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 667.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 28 sheets defined 49.6% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 416 through 426 removed outlier: 4.173A pdb=" N LYS A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.538A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.660A pdb=" N ASN A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.982A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 571 through 579 removed outlier: 4.555A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 4.174A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 730 removed outlier: 3.614A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 828 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 916 through 922 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.945A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 431 through 447 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 479 through 491 removed outlier: 4.020A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 531 through 541 removed outlier: 4.146A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 602 through 611 removed outlier: 4.335A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (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: 3.762A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 938 through 946 removed outlier: 3.853A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 428 removed outlier: 4.485A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 4.056A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 4.121A pdb=" N ASN C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.408A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 602 through 611 removed outlier: 4.342A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 619 removed outlier: 3.966A pdb=" N PHE C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.551A pdb=" N LYS C 726 " --> pdb=" O LYS C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 747 removed outlier: 3.961A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 825 Processing helix chain 'C' and resid 852 through 855 removed outlier: 3.659A pdb=" N SER C 855 " --> pdb=" O ASP C 852 " (cutoff:3.500A) No H-bonds generated for '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 922 Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.019A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 427 removed outlier: 4.606A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 467 removed outlier: 3.701A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 removed outlier: 4.234A pdb=" N ASP D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 512 removed outlier: 3.803A pdb=" N ARG D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 3.809A pdb=" N SER D 535 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 572 through 581 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 602 through 611 removed outlier: 4.230A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 645 removed outlier: 4.107A pdb=" N THR D 644 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 704 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 740 through 745 removed outlier: 4.355A pdb=" N GLN D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.976A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 425 removed outlier: 3.748A pdb=" N LEU E 425 " --> pdb=" O PHE E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 491 removed outlier: 3.647A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 591 through 595 removed outlier: 4.031A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 646 through 653 Processing helix chain 'E' and resid 662 through 673 removed outlier: 3.547A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 730 removed outlier: 3.562A pdb=" N LYS E 714 " --> pdb=" O ARG E 710 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 828 Processing helix chain 'E' and resid 852 through 855 removed outlier: 3.585A pdb=" N SER E 855 " --> pdb=" O ASP E 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 852 through 855' Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.904A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 428 removed outlier: 3.852A pdb=" N LEU F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.873A pdb=" N THR F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 530 through 541 removed outlier: 3.974A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 604 through 612 Processing helix chain 'F' and resid 612 through 617 removed outlier: 4.292A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 removed outlier: 3.730A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 682 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 741 through 745 Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 833 through 838 removed outlier: 3.572A pdb=" N THR F 837 " --> pdb=" O ASP F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 852 through 855 Processing helix chain 'F' and resid 856 through 869 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 938 through 947 removed outlier: 4.001A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 546 removed outlier: 6.745A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR A 638 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 589 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.899A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 771 Processing sheet with id=AA4, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AA5, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.608A pdb=" N GLU A 882 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 544 through 545 removed outlier: 7.029A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.891A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 765 through 769 removed outlier: 6.070A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 844 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 803 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 877 through 879 removed outlier: 7.093A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.812A pdb=" N GLU B 882 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 543 through 548 removed outlier: 6.441A pdb=" N GLU C 543 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU C 588 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP C 590 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE C 547 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE C 636 " --> pdb=" O PRO C 585 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE C 587 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR C 638 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS C 517 " --> pdb=" O PHE C 635 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N CYS C 637 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA C 639 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE C 521 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.609A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 765 through 767 removed outlier: 6.189A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 877 through 879 Processing sheet with id=AB6, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.601A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 543 through 548 removed outlier: 7.669A pdb=" N ILE D 636 " --> pdb=" O PRO D 585 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 689 through 690 removed outlier: 4.244A pdb=" N LYS D 690 " --> pdb=" O VAL D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 765 through 769 removed outlier: 6.491A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL D 844 " --> pdb=" O GLU D 801 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR D 803 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 877 through 879 removed outlier: 6.598A pdb=" N ALA D 878 " --> pdb=" O VAL D 911 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC3, first strand: chain 'E' and resid 545 through 548 removed outlier: 6.910A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.687A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 799 through 802 removed outlier: 6.171A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N LEU E 877 " --> pdb=" O VAL E 764 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET E 766 " --> pdb=" O LEU E 877 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET E 879 " --> pdb=" O MET E 766 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 768 " --> pdb=" O MET E 879 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 882 through 883 removed outlier: 3.689A pdb=" N GLU E 882 " --> pdb=" O LEU E 890 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.710A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 689 through 691 removed outlier: 3.643A pdb=" N LYS F 690 " --> pdb=" O VAL F 735 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 737 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 799 through 803 removed outlier: 6.236A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N LEU F 877 " --> pdb=" O VAL F 764 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET F 766 " --> pdb=" O LEU F 877 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 882 through 883 1099 hydrogen bonds defined for protein. 3207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.19 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: 8093 1.34 - 1.46: 4056 1.46 - 1.58: 12615 1.58 - 1.69: 26 1.69 - 1.81: 198 Bond restraints: 24988 Sorted by residual: bond pdb=" C4 ATP A1000 " pdb=" C5 ATP A1000 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C4 ATP D1001 " pdb=" C5 ATP D1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C4 ATP D1002 " pdb=" C5 ATP D1002 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C4 ATP B1000 " pdb=" C5 ATP B1000 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C5 ATP A1000 " pdb=" C6 ATP A1000 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.34e+01 ... (remaining 24983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 33710 3.98 - 7.97: 129 7.97 - 11.95: 10 11.95 - 15.93: 3 15.93 - 19.92: 5 Bond angle restraints: 33857 Sorted by residual: angle pdb=" PB ATP D1002 " pdb=" O3B ATP D1002 " pdb=" PG ATP D1002 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP B1000 " pdb=" O3B ATP B1000 " pdb=" PG ATP B1000 " ideal model delta sigma weight residual 139.87 121.21 18.66 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PA ATP B1000 " pdb=" O3A ATP B1000 " pdb=" PB ATP B1000 " ideal model delta sigma weight residual 136.83 118.72 18.11 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PB ATP A1000 " pdb=" O3B ATP A1000 " pdb=" PG ATP A1000 " ideal model delta sigma weight residual 139.87 123.37 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP D1001 " pdb=" O3B ATP D1001 " pdb=" PG ATP D1001 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 ... (remaining 33852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13688 17.99 - 35.98: 1291 35.98 - 53.97: 213 53.97 - 71.97: 67 71.97 - 89.96: 25 Dihedral angle restraints: 15284 sinusoidal: 6207 harmonic: 9077 Sorted by residual: dihedral pdb=" CA GLY A 571 " pdb=" C GLY A 571 " pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta harmonic sigma weight residual -180.00 -152.85 -27.15 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ARG E 874 " pdb=" C ARG E 874 " pdb=" N GLN E 875 " pdb=" CA GLN E 875 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ARG F 874 " pdb=" C ARG F 874 " pdb=" N GLN F 875 " pdb=" CA GLN F 875 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 15281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2356 0.037 - 0.073: 1102 0.073 - 0.110: 340 0.110 - 0.147: 89 0.147 - 0.183: 11 Chirality restraints: 3898 Sorted by residual: chirality pdb=" CB ILE A 573 " pdb=" CA ILE A 573 " pdb=" CG1 ILE A 573 " pdb=" CG2 ILE A 573 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA PRO E 585 " pdb=" N PRO E 585 " pdb=" C PRO E 585 " pdb=" CB PRO E 585 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ASN B 584 " pdb=" N ASN B 584 " pdb=" C ASN B 584 " pdb=" CB ASN B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 3895 not shown) Planarity restraints: 4327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 430 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 431 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 844 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO D 845 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 845 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 845 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 761 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO E 762 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 762 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 762 " -0.031 5.00e-02 4.00e+02 ... (remaining 4324 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 163 2.53 - 3.12: 18642 3.12 - 3.71: 37690 3.71 - 4.31: 54323 4.31 - 4.90: 90610 Nonbonded interactions: 201428 Sorted by model distance: nonbonded pdb=" OG1 THR D 530 " pdb="MG MG D1003 " model vdw 1.934 2.170 nonbonded pdb=" OG1 THR C 530 " pdb="MG MG C1001 " model vdw 1.937 2.170 nonbonded pdb=" O2B ATP A1000 " pdb="MG MG A1001 " model vdw 1.956 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1001 " model vdw 1.980 2.170 nonbonded pdb="MG MG C1001 " pdb=" O2G ATP D1001 " model vdw 1.999 2.170 ... (remaining 201423 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 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 459 or (resid 460 and (name N or name CA or name C or n \ ame O or name CB )) or resid 461 through 497 or (resid 498 and (name N or name C \ A or name C or name O or name CB )) or resid 499 or (resid 500 and (name N or na \ me CA or name C or name O or name CB )) or resid 501 through 510 or (resid 511 a \ nd (name N or name CA or name C or name O or name CB )) or resid 512 through 514 \ or (resid 515 and (name N or name CA or name C or name O or name CB )) or resid \ 516 through 589 or (resid 590 and (name N or name CA or name C or name O or nam \ e CB )) or resid 591 through 595 or resid 603 through 720 or (resid 721 and (nam \ e N or name CA or name C or name O or name CB )) or resid 722 through 783 or res \ id 796 or (resid 797 and (name N or name CA or name C or name O or name CB )) or \ resid 798 through 811 or (resid 812 and (name N or name CA or name C or name O \ or name CB )) or resid 813 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 827 or (resid 832 \ and (name N or name CA or name C or name O or name CB )) or resid 833 through 9 \ 28 or (resid 929 and (name N or name CA or name C or name O or name CB )) or res \ id 930 through 947)) selection = (chain 'B' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 through 502 or (res \ id 503 and (name N or name CA or name C or name O or name CB )) or resid 504 thr \ ough 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) \ or resid 512 through 514 or (resid 515 and (name N or name CA or name C or name \ O or name CB )) or resid 516 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 562 or (resid 563 and (name \ N or name CA or name C or name O or name CB )) or resid 564 through 571 or (res \ id 572 and (name N or name CA or name C or name O or name CB )) or resid 573 thr \ ough 589 or (resid 590 and (name N or name CA or name C or name O or name CB )) \ or resid 591 through 595 or resid 603 or (resid 604 and (name N or name CA or na \ me C or name O or name CB )) or resid 605 through 611 or (resid 612 and (name N \ or name CA or name C or name O or name CB )) or resid 613 or (resid 614 and (nam \ e N or name CA or name C or name O or name CB )) or resid 615 through 619 or (re \ sid 620 and (name N or name CA or name C or name O or name CB )) or resid 621 th \ rough 720 or (resid 721 and (name N or name CA or name C or name O or name CB )) \ or resid 722 through 753 or (resid 754 and (name N or name CA or name C or name \ O or name CB )) or resid 755 through 783 or resid 796 or (resid 797 and (name N \ or name CA or name C or name O or name CB )) or resid 798 through 821 or (resid \ 822 through 823 and (name N or name CA or name C or name O or name CB )) or res \ id 824 through 827 or (resid 832 and (name N or name CA or name C or name O or n \ ame CB )) or resid 833 through 947)) selection = (chain 'C' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 502 or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or resid 504 \ through 514 or (resid 515 and (name N or name CA or name C or name O or name CB \ )) or resid 516 through 556 or (resid 557 and (name N or name CA or name C or n \ ame O or name CB )) or resid 558 through 562 or (resid 563 and (name N or name C \ A or name C or name O or name CB )) or resid 564 through 571 or (resid 572 and ( \ name N or name CA or name C or name O or name CB )) or resid 573 through 589 or \ (resid 590 and (name N or name CA or name C or name O or name CB )) or resid 591 \ through 595 or resid 603 or (resid 604 and (name N or name CA or name C or name \ O or name CB )) or resid 605 through 611 or (resid 612 and (name N or name CA o \ r name C or name O or name CB )) or resid 613 or (resid 614 and (name N or name \ CA or name C or name O or name CB )) or resid 615 through 619 or (resid 620 and \ (name N or name CA or name C or name O or name CB )) or resid 621 through 720 or \ (resid 721 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 2 through 753 or (resid 754 and (name N or name CA or name C or name O or name C \ B )) or resid 755 through 783 or resid 796 or (resid 797 and (name N or name CA \ or name C or name O or name CB )) or resid 798 through 811 or (resid 812 and (na \ me N or name CA or name C or name O or name CB )) or resid 813 through 928 or (r \ esid 929 and (name N or name CA or name C or name O or name CB )) or resid 930 t \ hrough 947)) selection = (chain 'D' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 502 or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or resid 504 \ through 510 or (resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 514 or (resid 515 and (name N or name CA or name C or n \ ame O or name CB )) or resid 516 through 556 or (resid 557 and (name N or name C \ A or name C or name O or name CB )) or resid 558 through 562 or (resid 563 and ( \ name N or name CA or name C or name O or name CB )) or resid 564 through 571 or \ (resid 572 and (name N or name CA or name C or name O or name CB )) or resid 573 \ through 589 or (resid 590 and (name N or name CA or name C or name O or name CB \ )) or resid 591 through 595 or resid 603 or (resid 604 and (name N or name CA o \ r name C or name O or name CB )) or resid 605 through 611 or (resid 612 and (nam \ e N or name CA or name C or name O or name CB )) or resid 613 or (resid 614 and \ (name N or name CA or name C or name O or name CB )) or resid 615 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 720 or (resid 721 and (name N or name CA or name C or name O or name C \ B )) or resid 722 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 783 or resid 796 or (resid 797 and (na \ me N or name CA or name C or name O or name CB )) or resid 798 through 811 or (r \ esid 812 and (name N or name CA or name C or name O or name CB )) or resid 813 t \ hrough 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 827 or (resid 832 and (name N or name CA or n \ ame C or name O or name CB )) or resid 833 through 928 or (resid 929 and (name N \ or name CA or name C or name O or name CB )) or resid 930 through 947)) selection = (chain 'E' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 502 or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or resid 504 \ through 510 or (resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 514 or (resid 515 and (name N or name CA or name C or n \ ame O or name CB )) or resid 516 through 556 or (resid 557 and (name N or name C \ A or name C or name O or name CB )) or resid 558 through 562 or (resid 563 and ( \ name N or name CA or name C or name O or name CB )) or resid 564 through 571 or \ (resid 572 and (name N or name CA or name C or name O or name CB )) or resid 573 \ through 595 or resid 603 or (resid 604 and (name N or name CA or name C or name \ O or name CB )) or resid 605 through 611 or (resid 612 and (name N or name CA o \ r name C or name O or name CB )) or resid 613 or (resid 614 and (name N or name \ CA or name C or name O or name CB )) or resid 615 through 619 or (resid 620 and \ (name N or name CA or name C or name O or name CB )) or resid 621 through 720 or \ (resid 721 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 2 through 753 or (resid 754 and (name N or name CA or name C or name O or name C \ B )) or resid 755 through 783 or resid 796 through 811 or (resid 812 and (name N \ or name CA or name C or name O or name CB )) or resid 813 through 821 or (resid \ 822 through 823 and (name N or name CA or name C or name O or name CB )) or res \ id 824 through 827 or (resid 832 and (name N or name CA or name C or name O or n \ ame CB )) or resid 833 through 928 or (resid 929 and (name N or name CA or name \ C or name O or name CB )) or resid 930 through 947)) selection = (chain 'F' and (resid 420 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 446 or (resid 447 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 or (resid \ 450 through 452 and (name N or name CA or name C or name O or name CB )) or resi \ d 453 through 463 or (resid 464 and (name N or name CA or name C or name O or na \ me CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or name C \ or name O or name CB )) or resid 491 through 502 or (resid 503 and (name N or n \ ame CA or name C or name O or name CB )) or resid 504 through 510 or (resid 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 55 \ 6 or (resid 557 and (name N or name CA or name C or name O or name CB )) or resi \ d 558 through 562 or (resid 563 and (name N or name CA or name C or name O or na \ me CB )) or resid 564 through 571 or (resid 572 and (name N or name CA or name C \ or name O or name CB )) or resid 573 through 589 or (resid 590 and (name N or n \ ame CA or name C or name O or name CB )) or resid 591 through 603 or (resid 604 \ and (name N or name CA or name C or name O or name CB )) or resid 605 through 61 \ 1 or (resid 612 and (name N or name CA or name C or name O or name CB )) or resi \ d 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or \ resid 615 through 619 or (resid 620 and (name N or name CA or name C or name O o \ r name CB )) or resid 621 through 753 or (resid 754 and (name N or name CA or na \ me C or name O or name CB )) or resid 755 through 783 or resid 796 through 811 o \ r (resid 812 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 13 through 821 or (resid 822 through 823 and (name N or name CA or name C or nam \ e O or name CB )) or resid 824 through 827 or (resid 832 and (name N or name CA \ or name C or name O or name CB )) or resid 833 through 928 or (resid 929 and (na \ me N or name CA or name C or name O or name CB )) or resid 930 through 947)) } 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 individual isotropic 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.990 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.079 24990 Z= 0.325 Angle : 0.792 19.915 33857 Z= 0.499 Chirality : 0.046 0.183 3898 Planarity : 0.005 0.067 4327 Dihedral : 14.831 89.957 9440 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.08 % Allowed : 7.68 % Favored : 92.24 % 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: -2.42 (0.13), residues: 3109 helix: -0.76 (0.12), residues: 1389 sheet: -1.20 (0.24), residues: 403 loop : -2.66 (0.14), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 721 TYR 0.018 0.002 TYR E 939 PHE 0.020 0.002 PHE A 820 TRP 0.011 0.002 TRP C 470 HIS 0.013 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00680 (24988) covalent geometry : angle 0.79189 (33857) hydrogen bonds : bond 0.08770 ( 1099) hydrogen bonds : angle 5.30425 ( 3207) Misc. bond : bond 0.00263 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: B 552 MET cc_start: 0.9045 (ttm) cc_final: 0.8765 (ttp) REVERT: B 600 GLN cc_start: 0.6236 (mp10) cc_final: 0.6030 (mp10) REVERT: C 420 LYS cc_start: 0.8293 (ttpt) cc_final: 0.8085 (tttp) REVERT: E 681 LEU cc_start: 0.8848 (mm) cc_final: 0.8639 (mm) REVERT: E 810 MET cc_start: 0.8828 (tpt) cc_final: 0.8419 (tpt) REVERT: F 563 ARG cc_start: 0.7284 (mtp180) cc_final: 0.7014 (mtt90) outliers start: 2 outliers final: 1 residues processed: 309 average time/residue: 0.1785 time to fit residues: 81.5544 Evaluate side-chains 235 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 580 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 491 HIS A 622 HIS B 456 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 702 GLN B 839 HIS C 433 HIS ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN D 451 HIS D 456 ASN D 477 ASN D 615 GLN D 841 HIS D 876 ASN E 450 ASN E 515 GLN E 916 ASN F 616 ASN F 702 GLN F 743 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085534 restraints weight = 41852.975| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.88 r_work: 0.2855 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24990 Z= 0.116 Angle : 0.550 9.466 33857 Z= 0.277 Chirality : 0.041 0.169 3898 Planarity : 0.005 0.062 4327 Dihedral : 7.752 79.840 3563 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.41 % Allowed : 10.73 % Favored : 87.87 % 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: -0.88 (0.14), residues: 3109 helix: 0.72 (0.13), residues: 1399 sheet: -0.75 (0.25), residues: 405 loop : -2.00 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 459 TYR 0.014 0.001 TYR E 939 PHE 0.019 0.001 PHE F 455 TRP 0.009 0.001 TRP C 470 HIS 0.007 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00270 (24988) covalent geometry : angle 0.54986 (33857) hydrogen bonds : bond 0.03240 ( 1099) hydrogen bonds : angle 4.56532 ( 3207) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7784 (p0) cc_final: 0.7437 (t0) REVERT: A 621 ASP cc_start: 0.8152 (t70) cc_final: 0.7933 (t0) REVERT: B 552 MET cc_start: 0.9035 (ttm) cc_final: 0.8806 (ttp) REVERT: B 600 GLN cc_start: 0.6248 (mp10) cc_final: 0.5997 (mp10) REVERT: B 756 MET cc_start: 0.8386 (ttm) cc_final: 0.8177 (ttm) REVERT: B 768 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8105 (pp) REVERT: C 420 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8167 (tttp) REVERT: C 597 ARG cc_start: 0.7526 (ptp90) cc_final: 0.7099 (ptp-110) REVERT: D 552 MET cc_start: 0.9281 (ttp) cc_final: 0.8913 (ttp) REVERT: D 897 GLU cc_start: 0.8369 (mp0) cc_final: 0.8141 (mp0) REVERT: E 576 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7754 (p) REVERT: E 681 LEU cc_start: 0.8972 (mm) cc_final: 0.8760 (mm) REVERT: F 488 GLU cc_start: 0.7776 (pp20) cc_final: 0.7511 (pp20) REVERT: F 557 GLU cc_start: 0.6961 (mp0) cc_final: 0.6668 (mp0) REVERT: F 562 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7018 (mtm-85) REVERT: F 563 ARG cc_start: 0.7426 (mtp180) cc_final: 0.7031 (mtt90) REVERT: F 610 LEU cc_start: 0.8841 (tp) cc_final: 0.8593 (tp) REVERT: F 650 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7308 (mtp180) outliers start: 37 outliers final: 24 residues processed: 301 average time/residue: 0.1612 time to fit residues: 75.0611 Evaluate side-chains 269 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 809 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 78 optimal weight: 0.0020 chunk 35 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 overall best weight: 5.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS A 460 ASN B 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 477 ASN E 839 HIS F 841 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.082783 restraints weight = 42173.889| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.97 r_work: 0.2789 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24990 Z= 0.209 Angle : 0.608 9.527 33857 Z= 0.306 Chirality : 0.044 0.164 3898 Planarity : 0.005 0.064 4327 Dihedral : 7.909 79.647 3563 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.51 % Allowed : 12.59 % Favored : 84.90 % 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: -0.51 (0.15), residues: 3109 helix: 1.03 (0.14), residues: 1399 sheet: -0.55 (0.26), residues: 399 loop : -1.81 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 459 TYR 0.016 0.002 TYR E 939 PHE 0.018 0.002 PHE F 820 TRP 0.008 0.001 TRP C 470 HIS 0.005 0.001 HIS D 828 Details of bonding type rmsd covalent geometry : bond 0.00514 (24988) covalent geometry : angle 0.60828 (33857) hydrogen bonds : bond 0.03854 ( 1099) hydrogen bonds : angle 4.60051 ( 3207) Misc. bond : bond 0.00189 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 248 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7824 (p0) cc_final: 0.7427 (t0) REVERT: A 590 ASP cc_start: 0.7229 (t0) cc_final: 0.6901 (t0) REVERT: A 931 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8426 (pp) REVERT: B 552 MET cc_start: 0.9034 (ttm) cc_final: 0.8809 (ttp) REVERT: B 600 GLN cc_start: 0.6311 (mp10) cc_final: 0.6050 (mp10) REVERT: B 768 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8153 (pp) REVERT: B 879 MET cc_start: 0.7898 (ptp) cc_final: 0.7658 (ptp) REVERT: C 420 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8182 (tttp) REVERT: D 897 GLU cc_start: 0.8524 (mp0) cc_final: 0.8277 (mp0) REVERT: E 448 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8342 (mm) REVERT: E 681 LEU cc_start: 0.8843 (mm) cc_final: 0.8632 (mm) REVERT: F 557 GLU cc_start: 0.7073 (mp0) cc_final: 0.6762 (mp0) REVERT: F 562 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7056 (mtm-85) REVERT: F 563 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7021 (mtt90) REVERT: F 616 ASN cc_start: 0.7709 (m-40) cc_final: 0.7486 (m110) REVERT: F 654 GLU cc_start: 0.6632 (tt0) cc_final: 0.6331 (tt0) REVERT: F 852 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7573 (p0) outliers start: 66 outliers final: 47 residues processed: 290 average time/residue: 0.1597 time to fit residues: 71.4566 Evaluate side-chains 291 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 744 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 581 LYS Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 262 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 299 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.082468 restraints weight = 42124.293| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.95 r_work: 0.2797 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24990 Z= 0.190 Angle : 0.591 9.839 33857 Z= 0.296 Chirality : 0.043 0.163 3898 Planarity : 0.005 0.063 4327 Dihedral : 7.842 80.111 3563 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.27 % Allowed : 13.88 % Favored : 82.85 % 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: -0.26 (0.15), residues: 3109 helix: 1.24 (0.14), residues: 1398 sheet: -0.45 (0.26), residues: 402 loop : -1.68 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 459 TYR 0.015 0.002 TYR E 939 PHE 0.019 0.002 PHE A 547 TRP 0.009 0.001 TRP C 470 HIS 0.005 0.001 HIS D 828 Details of bonding type rmsd covalent geometry : bond 0.00468 (24988) covalent geometry : angle 0.59075 (33857) hydrogen bonds : bond 0.03712 ( 1099) hydrogen bonds : angle 4.52834 ( 3207) Misc. bond : bond 0.00152 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 255 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7717 (p0) cc_final: 0.7389 (t0) REVERT: A 778 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 808 GLU cc_start: 0.7072 (tp30) cc_final: 0.6856 (tp30) REVERT: A 931 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8385 (pp) REVERT: B 439 ASP cc_start: 0.8018 (m-30) cc_final: 0.7707 (m-30) REVERT: B 552 MET cc_start: 0.9019 (ttm) cc_final: 0.8792 (ttp) REVERT: B 600 GLN cc_start: 0.6166 (mp10) cc_final: 0.5913 (mp10) REVERT: B 768 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8279 (pp) REVERT: B 778 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7441 (mt) REVERT: B 826 MET cc_start: 0.6974 (ppp) cc_final: 0.6724 (ppp) REVERT: C 420 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8184 (tttp) REVERT: C 597 ARG cc_start: 0.7932 (ptp90) cc_final: 0.7731 (ptp90) REVERT: D 552 MET cc_start: 0.9328 (ttp) cc_final: 0.9030 (ttp) REVERT: D 897 GLU cc_start: 0.8555 (mp0) cc_final: 0.8299 (mp0) REVERT: E 448 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8367 (mm) REVERT: E 543 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8534 (mm-30) REVERT: E 810 MET cc_start: 0.9050 (tpt) cc_final: 0.8675 (tpt) REVERT: F 455 PHE cc_start: 0.6341 (t80) cc_final: 0.6081 (t80) REVERT: F 557 GLU cc_start: 0.7012 (mp0) cc_final: 0.6794 (mp0) REVERT: F 562 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7092 (mtm-85) REVERT: F 563 ARG cc_start: 0.7383 (mtp180) cc_final: 0.6993 (mtt90) REVERT: F 575 GLN cc_start: 0.8741 (mt0) cc_final: 0.8133 (mt0) REVERT: F 616 ASN cc_start: 0.7688 (m-40) cc_final: 0.7437 (m110) REVERT: F 644 THR cc_start: 0.8519 (t) cc_final: 0.8158 (p) REVERT: F 705 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7431 (mmt90) REVERT: F 852 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7619 (p0) outliers start: 86 outliers final: 61 residues processed: 317 average time/residue: 0.1660 time to fit residues: 81.2784 Evaluate side-chains 314 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 246 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 744 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 463 ASP Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 275 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 290 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 42 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 827 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.083652 restraints weight = 42033.664| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.96 r_work: 0.2815 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24990 Z= 0.144 Angle : 0.556 9.653 33857 Z= 0.278 Chirality : 0.042 0.148 3898 Planarity : 0.005 0.062 4327 Dihedral : 7.677 81.557 3563 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.04 % Allowed : 14.95 % Favored : 82.01 % 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: -0.00 (0.15), residues: 3109 helix: 1.44 (0.14), residues: 1406 sheet: -0.34 (0.26), residues: 409 loop : -1.54 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 459 TYR 0.014 0.001 TYR D 939 PHE 0.020 0.001 PHE A 547 TRP 0.009 0.001 TRP C 470 HIS 0.004 0.001 HIS D 828 Details of bonding type rmsd covalent geometry : bond 0.00349 (24988) covalent geometry : angle 0.55628 (33857) hydrogen bonds : bond 0.03386 ( 1099) hydrogen bonds : angle 4.40328 ( 3207) Misc. bond : bond 0.00118 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7671 (p0) cc_final: 0.7350 (t0) REVERT: A 590 ASP cc_start: 0.7251 (t0) cc_final: 0.6958 (t0) REVERT: A 685 ASP cc_start: 0.7900 (t70) cc_final: 0.7385 (p0) REVERT: A 778 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 931 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8376 (pp) REVERT: B 439 ASP cc_start: 0.8002 (m-30) cc_final: 0.7700 (m-30) REVERT: B 552 MET cc_start: 0.8988 (ttm) cc_final: 0.8749 (ttp) REVERT: B 600 GLN cc_start: 0.6150 (mp10) cc_final: 0.5890 (mp10) REVERT: B 768 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8379 (pp) REVERT: B 778 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7407 (mt) REVERT: B 826 MET cc_start: 0.6982 (ppp) cc_final: 0.6716 (ppp) REVERT: C 420 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8189 (tttp) REVERT: D 552 MET cc_start: 0.9327 (ttp) cc_final: 0.8973 (ttp) REVERT: D 897 GLU cc_start: 0.8555 (mp0) cc_final: 0.8294 (mp0) REVERT: E 448 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8355 (mm) REVERT: E 543 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8554 (mm-30) REVERT: F 455 PHE cc_start: 0.6278 (t80) cc_final: 0.6065 (t80) REVERT: F 476 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7611 (mt-10) REVERT: F 557 GLU cc_start: 0.7039 (mp0) cc_final: 0.6653 (mp0) REVERT: F 562 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7048 (mtm-85) REVERT: F 563 ARG cc_start: 0.7483 (mtp180) cc_final: 0.7082 (mtt90) REVERT: F 575 GLN cc_start: 0.8785 (mt0) cc_final: 0.8287 (mt0) REVERT: F 616 ASN cc_start: 0.7668 (m-40) cc_final: 0.7392 (m110) REVERT: F 644 THR cc_start: 0.8500 (t) cc_final: 0.8130 (p) REVERT: F 705 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7496 (mmt90) REVERT: F 852 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7724 (p0) outliers start: 80 outliers final: 60 residues processed: 313 average time/residue: 0.1694 time to fit residues: 81.3898 Evaluate side-chains 313 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 744 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 463 ASP Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 290 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 246 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.084323 restraints weight = 41829.545| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.95 r_work: 0.2827 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24990 Z= 0.136 Angle : 0.543 9.506 33857 Z= 0.272 Chirality : 0.042 0.145 3898 Planarity : 0.004 0.062 4327 Dihedral : 7.571 84.152 3563 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.42 % Allowed : 14.80 % Favored : 81.78 % 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: 0.18 (0.15), residues: 3109 helix: 1.59 (0.14), residues: 1407 sheet: -0.29 (0.26), residues: 413 loop : -1.43 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 459 TYR 0.014 0.001 TYR D 939 PHE 0.019 0.001 PHE A 547 TRP 0.008 0.001 TRP C 470 HIS 0.004 0.001 HIS E 828 Details of bonding type rmsd covalent geometry : bond 0.00328 (24988) covalent geometry : angle 0.54291 (33857) hydrogen bonds : bond 0.03268 ( 1099) hydrogen bonds : angle 4.33637 ( 3207) Misc. bond : bond 0.00112 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 255 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7579 (p0) cc_final: 0.7270 (t0) REVERT: A 575 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: A 590 ASP cc_start: 0.7160 (t0) cc_final: 0.6865 (t0) REVERT: A 685 ASP cc_start: 0.7882 (t70) cc_final: 0.7328 (p0) REVERT: A 778 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8591 (pp) REVERT: A 931 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (pp) REVERT: B 439 ASP cc_start: 0.8012 (m-30) cc_final: 0.7706 (m-30) REVERT: B 552 MET cc_start: 0.8950 (ttm) cc_final: 0.8713 (ttp) REVERT: B 600 GLN cc_start: 0.5997 (mp10) cc_final: 0.5716 (mp10) REVERT: B 768 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8439 (pp) REVERT: B 778 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7383 (mt) REVERT: B 826 MET cc_start: 0.7040 (ppp) cc_final: 0.6772 (ppp) REVERT: C 420 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8167 (tttp) REVERT: D 419 GLU cc_start: 0.6259 (mp0) cc_final: 0.5971 (mp0) REVERT: D 681 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 897 GLU cc_start: 0.8553 (mp0) cc_final: 0.8294 (mp0) REVERT: E 448 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8349 (mm) REVERT: E 576 CYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7771 (p) REVERT: E 810 MET cc_start: 0.9051 (tpt) cc_final: 0.8667 (tpt) REVERT: F 476 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7589 (mt-10) REVERT: F 557 GLU cc_start: 0.6922 (mp0) cc_final: 0.6539 (mp0) REVERT: F 562 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7281 (ttm110) REVERT: F 563 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7166 (mtt90) REVERT: F 575 GLN cc_start: 0.8784 (mt0) cc_final: 0.8288 (mt0) REVERT: F 608 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7800 (mm) REVERT: F 616 ASN cc_start: 0.7631 (m-40) cc_final: 0.7334 (m110) REVERT: F 644 THR cc_start: 0.8438 (t) cc_final: 0.8056 (p) REVERT: F 852 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7676 (p0) outliers start: 90 outliers final: 63 residues processed: 317 average time/residue: 0.1681 time to fit residues: 82.2935 Evaluate side-chains 314 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 241 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 744 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 180 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 162 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.083898 restraints weight = 41889.725| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.99 r_work: 0.2819 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24990 Z= 0.149 Angle : 0.558 9.424 33857 Z= 0.278 Chirality : 0.042 0.150 3898 Planarity : 0.005 0.061 4327 Dihedral : 7.598 85.842 3563 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.27 % Allowed : 15.14 % Favored : 81.59 % 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: 0.22 (0.15), residues: 3109 helix: 1.60 (0.14), residues: 1414 sheet: -0.23 (0.26), residues: 413 loop : -1.41 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 459 TYR 0.014 0.001 TYR D 939 PHE 0.022 0.001 PHE A 547 TRP 0.008 0.001 TRP C 470 HIS 0.004 0.001 HIS D 828 Details of bonding type rmsd covalent geometry : bond 0.00364 (24988) covalent geometry : angle 0.55760 (33857) hydrogen bonds : bond 0.03334 ( 1099) hydrogen bonds : angle 4.32993 ( 3207) Misc. bond : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 244 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7530 (p0) cc_final: 0.7329 (t0) REVERT: A 575 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: A 685 ASP cc_start: 0.7897 (t70) cc_final: 0.7317 (p0) REVERT: A 766 MET cc_start: 0.8706 (ttp) cc_final: 0.8389 (ttp) REVERT: A 778 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 931 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8247 (pp) REVERT: B 439 ASP cc_start: 0.8030 (m-30) cc_final: 0.7822 (m-30) REVERT: B 552 MET cc_start: 0.8951 (ttm) cc_final: 0.8711 (ttp) REVERT: B 600 GLN cc_start: 0.5986 (mp10) cc_final: 0.5703 (mp10) REVERT: B 768 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 778 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7359 (mt) REVERT: B 826 MET cc_start: 0.7052 (ppp) cc_final: 0.6777 (ppp) REVERT: C 420 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8190 (tttp) REVERT: D 419 GLU cc_start: 0.6299 (mp0) cc_final: 0.5998 (mp0) REVERT: D 451 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.6716 (m90) REVERT: D 681 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8132 (mp) REVERT: D 897 GLU cc_start: 0.8569 (mp0) cc_final: 0.8301 (mp0) REVERT: E 448 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8333 (mm) REVERT: E 810 MET cc_start: 0.9047 (tpt) cc_final: 0.8663 (tpt) REVERT: F 476 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7581 (mt-10) REVERT: F 557 GLU cc_start: 0.6933 (mp0) cc_final: 0.6570 (mp0) REVERT: F 563 ARG cc_start: 0.7499 (mtp180) cc_final: 0.7218 (mtt90) REVERT: F 608 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7817 (mm) REVERT: F 616 ASN cc_start: 0.7623 (m-40) cc_final: 0.7318 (m110) REVERT: F 644 THR cc_start: 0.8419 (t) cc_final: 0.8033 (p) REVERT: F 852 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7701 (p0) outliers start: 86 outliers final: 70 residues processed: 304 average time/residue: 0.1598 time to fit residues: 75.7605 Evaluate side-chains 320 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 744 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 941 GLU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 257 optimal weight: 0.6980 chunk 85 optimal weight: 0.0770 chunk 65 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 805 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085314 restraints weight = 41808.803| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.95 r_work: 0.2848 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24990 Z= 0.110 Angle : 0.533 13.150 33857 Z= 0.263 Chirality : 0.041 0.176 3898 Planarity : 0.004 0.061 4327 Dihedral : 7.429 89.379 3563 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.00 % Allowed : 15.44 % Favored : 81.55 % 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: 0.42 (0.15), residues: 3109 helix: 1.75 (0.14), residues: 1416 sheet: -0.15 (0.26), residues: 412 loop : -1.29 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 459 TYR 0.012 0.001 TYR E 939 PHE 0.026 0.001 PHE A 547 TRP 0.008 0.001 TRP C 470 HIS 0.014 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00258 (24988) covalent geometry : angle 0.53332 (33857) hydrogen bonds : bond 0.02983 ( 1099) hydrogen bonds : angle 4.20938 ( 3207) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7498 (p0) cc_final: 0.7295 (t0) REVERT: A 685 ASP cc_start: 0.7855 (t70) cc_final: 0.7293 (p0) REVERT: A 766 MET cc_start: 0.8634 (ttp) cc_final: 0.8309 (ttp) REVERT: A 778 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8567 (pp) REVERT: A 931 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8293 (pp) REVERT: B 435 MET cc_start: 0.8594 (tpt) cc_final: 0.7889 (tpt) REVERT: B 439 ASP cc_start: 0.8049 (m-30) cc_final: 0.7523 (m-30) REVERT: B 517 LYS cc_start: 0.8950 (mmtt) cc_final: 0.7877 (mtmt) REVERT: B 552 MET cc_start: 0.8905 (ttm) cc_final: 0.8643 (ttp) REVERT: B 600 GLN cc_start: 0.6118 (mp10) cc_final: 0.5875 (mp10) REVERT: B 768 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8436 (pp) REVERT: B 826 MET cc_start: 0.7003 (ppp) cc_final: 0.6739 (ppp) REVERT: C 420 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8162 (tttp) REVERT: D 419 GLU cc_start: 0.6343 (mp0) cc_final: 0.6077 (mp0) REVERT: D 897 GLU cc_start: 0.8631 (mp0) cc_final: 0.8343 (mp0) REVERT: E 448 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8604 (tp) REVERT: E 576 CYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7765 (p) REVERT: F 435 MET cc_start: 0.6934 (tpt) cc_final: 0.6680 (tpt) REVERT: F 439 ASP cc_start: 0.6995 (t0) cc_final: 0.6129 (p0) REVERT: F 476 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7563 (mt-10) REVERT: F 557 GLU cc_start: 0.6927 (mp0) cc_final: 0.6467 (mp0) REVERT: F 562 ARG cc_start: 0.7169 (ttm110) cc_final: 0.6845 (ttm110) REVERT: F 563 ARG cc_start: 0.7411 (mtp180) cc_final: 0.7087 (mtt90) REVERT: F 608 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7839 (mm) REVERT: F 616 ASN cc_start: 0.7635 (m-40) cc_final: 0.7319 (m110) REVERT: F 644 THR cc_start: 0.8415 (t) cc_final: 0.8064 (p) REVERT: F 852 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7683 (p0) outliers start: 79 outliers final: 59 residues processed: 315 average time/residue: 0.1499 time to fit residues: 74.1261 Evaluate side-chains 311 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 245 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 941 GLU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 300 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 251 optimal weight: 0.9980 chunk 305 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 477 ASN E 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.084516 restraints weight = 42098.804| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.96 r_work: 0.2834 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24990 Z= 0.136 Angle : 0.553 12.870 33857 Z= 0.274 Chirality : 0.042 0.199 3898 Planarity : 0.004 0.061 4327 Dihedral : 7.476 89.720 3563 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.97 % Allowed : 15.67 % Favored : 81.36 % 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: 0.44 (0.15), residues: 3109 helix: 1.76 (0.14), residues: 1415 sheet: -0.14 (0.26), residues: 412 loop : -1.27 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 422 TYR 0.014 0.001 TYR D 939 PHE 0.026 0.001 PHE A 547 TRP 0.013 0.001 TRP F 470 HIS 0.003 0.001 HIS E 839 Details of bonding type rmsd covalent geometry : bond 0.00331 (24988) covalent geometry : angle 0.55295 (33857) hydrogen bonds : bond 0.03183 ( 1099) hydrogen bonds : angle 4.24307 ( 3207) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8445 (mmmm) REVERT: A 685 ASP cc_start: 0.7851 (t70) cc_final: 0.7295 (p0) REVERT: A 778 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 931 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8291 (pp) REVERT: B 435 MET cc_start: 0.8589 (tpt) cc_final: 0.7743 (tpt) REVERT: B 439 ASP cc_start: 0.8004 (m-30) cc_final: 0.7466 (m-30) REVERT: B 552 MET cc_start: 0.8917 (ttm) cc_final: 0.8648 (ttp) REVERT: B 600 GLN cc_start: 0.6103 (mp10) cc_final: 0.5863 (mp10) REVERT: B 768 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8447 (pp) REVERT: B 778 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7334 (mt) REVERT: B 826 MET cc_start: 0.7022 (ppp) cc_final: 0.6751 (ppp) REVERT: C 420 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8179 (tttp) REVERT: D 419 GLU cc_start: 0.6284 (mp0) cc_final: 0.5993 (mp0) REVERT: D 451 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6805 (m90) REVERT: D 681 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8134 (mp) REVERT: D 897 GLU cc_start: 0.8659 (mp0) cc_final: 0.8371 (mp0) REVERT: E 448 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8279 (mm) REVERT: F 435 MET cc_start: 0.6846 (tpt) cc_final: 0.6545 (tpt) REVERT: F 439 ASP cc_start: 0.7010 (t0) cc_final: 0.6135 (p0) REVERT: F 476 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7566 (mt-10) REVERT: F 557 GLU cc_start: 0.6716 (mp0) cc_final: 0.6063 (mp0) REVERT: F 563 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7005 (mtt90) REVERT: F 608 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7842 (mm) REVERT: F 616 ASN cc_start: 0.7622 (m-40) cc_final: 0.7304 (m110) REVERT: F 644 THR cc_start: 0.8463 (t) cc_final: 0.8091 (p) REVERT: F 852 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7598 (p0) outliers start: 78 outliers final: 65 residues processed: 298 average time/residue: 0.1637 time to fit residues: 75.7466 Evaluate side-chains 317 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 941 GLU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 212 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 180 optimal weight: 0.7980 chunk 252 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.086501 restraints weight = 41583.988| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.00 r_work: 0.2857 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24990 Z= 0.099 Angle : 0.528 12.588 33857 Z= 0.260 Chirality : 0.040 0.190 3898 Planarity : 0.004 0.061 4327 Dihedral : 7.267 87.532 3563 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.47 % Allowed : 16.20 % Favored : 81.32 % 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: 0.62 (0.15), residues: 3109 helix: 1.92 (0.14), residues: 1415 sheet: -0.07 (0.26), residues: 409 loop : -1.18 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 422 TYR 0.010 0.001 TYR E 939 PHE 0.024 0.001 PHE A 547 TRP 0.010 0.001 TRP F 470 HIS 0.009 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00228 (24988) covalent geometry : angle 0.52838 (33857) hydrogen bonds : bond 0.02798 ( 1099) hydrogen bonds : angle 4.12698 ( 3207) Misc. bond : bond 0.00082 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 268 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.6643 (mmp80) cc_final: 0.6380 (mmp80) REVERT: A 578 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8317 (mmmm) REVERT: A 685 ASP cc_start: 0.7829 (t70) cc_final: 0.7282 (p0) REVERT: A 766 MET cc_start: 0.8581 (ttp) cc_final: 0.8224 (ttp) REVERT: A 778 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8570 (pp) REVERT: B 435 MET cc_start: 0.8613 (tpt) cc_final: 0.7959 (tpt) REVERT: B 439 ASP cc_start: 0.8029 (m-30) cc_final: 0.7495 (m-30) REVERT: B 517 LYS cc_start: 0.8904 (mmtt) cc_final: 0.7886 (mtmt) REVERT: B 552 MET cc_start: 0.8875 (ttm) cc_final: 0.8623 (ttp) REVERT: B 768 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8412 (pp) REVERT: B 778 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7225 (mt) REVERT: B 826 MET cc_start: 0.6996 (ppp) cc_final: 0.6718 (ppp) REVERT: C 420 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8203 (tttp) REVERT: D 419 GLU cc_start: 0.6291 (mp0) cc_final: 0.6030 (mp0) REVERT: D 681 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8100 (mp) REVERT: D 897 GLU cc_start: 0.8653 (mp0) cc_final: 0.8306 (mp0) REVERT: E 448 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8601 (tp) REVERT: E 489 GLU cc_start: 0.8319 (tt0) cc_final: 0.8045 (mt-10) REVERT: E 576 CYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7846 (p) REVERT: F 435 MET cc_start: 0.6750 (tpt) cc_final: 0.6446 (tpt) REVERT: F 439 ASP cc_start: 0.6897 (t0) cc_final: 0.6111 (p0) REVERT: F 476 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7576 (mt-10) REVERT: F 557 GLU cc_start: 0.6679 (mp0) cc_final: 0.5945 (mp0) REVERT: F 563 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6834 (mtt90) REVERT: F 616 ASN cc_start: 0.7609 (m-40) cc_final: 0.7287 (m110) REVERT: F 644 THR cc_start: 0.8365 (t) cc_final: 0.8004 (p) REVERT: F 852 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7601 (p0) outliers start: 65 outliers final: 50 residues processed: 309 average time/residue: 0.1658 time to fit residues: 77.8425 Evaluate side-chains 313 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 477 ASN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 941 GLU Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 200 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 204 optimal weight: 0.0670 overall best weight: 4.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086460 restraints weight = 41741.092| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.99 r_work: 0.2858 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 24990 Z= 0.148 Angle : 0.677 59.040 33857 Z= 0.371 Chirality : 0.042 0.638 3898 Planarity : 0.004 0.060 4327 Dihedral : 7.281 87.527 3563 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.28 % Allowed : 16.47 % Favored : 81.25 % Cbeta Deviations : 0.03 % 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: 0.61 (0.15), residues: 3109 helix: 1.91 (0.14), residues: 1415 sheet: -0.06 (0.26), residues: 409 loop : -1.18 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 546 TYR 0.010 0.001 TYR D 939 PHE 0.024 0.001 PHE A 547 TRP 0.008 0.001 TRP F 470 HIS 0.006 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00311 (24988) covalent geometry : angle 0.67709 (33857) hydrogen bonds : bond 0.02841 ( 1099) hydrogen bonds : angle 4.12688 ( 3207) Misc. bond : bond 0.00107 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4492.20 seconds wall clock time: 77 minutes 57.53 seconds (4677.53 seconds total)