Starting phenix.real_space_refine on Wed Mar 4 19:00:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f5b_31464/03_2026/7f5b_31464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f5b_31464/03_2026/7f5b_31464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f5b_31464/03_2026/7f5b_31464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f5b_31464/03_2026/7f5b_31464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f5b_31464/03_2026/7f5b_31464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f5b_31464/03_2026/7f5b_31464.map" } resolution = 3.9 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= 0.003 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 97 5.16 5 C 9876 2.51 5 N 2489 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15328 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3454 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 419} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3416 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 415} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3458 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain: "D" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3315 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 402} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1506 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGT:plan-1': 1, 'PGT:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.51, per 1000 atoms: 0.23 Number of scatterers: 15328 At special positions: 0 Unit cell: (121.04, 116.96, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 97 16.00 O 2865 8.00 N 2489 7.00 C 9876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=2.01 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.02 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.04 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1001 " - " ASN A 751 " " NAG A1002 " - " ASN A 546 " " NAG B1102 " - " ASN B 751 " " NAG C1001 " - " ASN C 546 " " NAG C1002 " - " ASN C 751 " " NAG D1001 " - " ASN D 751 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN D 546 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 729.7 milliseconds 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 20 sheets defined 48.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.505A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.531A pdb=" N TRP A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.878A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.508A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 697 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 773 through 789 removed outlier: 4.530A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 824 through 851 removed outlier: 3.599A pdb=" N ASN A 849 " --> pdb=" O LYS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 866 removed outlier: 4.343A pdb=" N SER A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 454 removed outlier: 4.035A pdb=" N TYR B 454 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.932A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.123A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.972A pdb=" N PHE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.722A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.671A pdb=" N MET B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 662 removed outlier: 3.507A pdb=" N ILE B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 688 through 695 removed outlier: 3.592A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 4.156A pdb=" N MET B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 773 through 789 removed outlier: 4.209A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 816 through 821 removed outlier: 3.556A pdb=" N ILE B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.824A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 863 removed outlier: 3.529A pdb=" N SER B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 462 through 475 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.632A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 526 removed outlier: 4.288A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 583 Processing helix chain 'C' and resid 607 through 621 Processing helix chain 'C' and resid 630 through 663 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 690 through 697 removed outlier: 3.693A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 713 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 747 Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.716A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 Processing helix chain 'C' and resid 824 through 848 removed outlier: 3.541A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.879A pdb=" N MET C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 removed outlier: 3.741A pdb=" N ASP D 457 " --> pdb=" O TYR D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 457' Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.682A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.940A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.713A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.766A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 620 removed outlier: 3.557A pdb=" N MET D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 661 removed outlier: 3.884A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.709A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 670 through 675' Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 702 through 712 Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 removed outlier: 4.399A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.819A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 4.054A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.708A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 344 Processing helix chain 'E' and resid 347 through 372 removed outlier: 3.826A pdb=" N VAL E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 478 through 482 removed outlier: 3.904A pdb=" N LEU A 512 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 removed outlier: 3.600A pdb=" N LYS A 762 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AA6, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.876A pdb=" N THR B 437 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'B' and resid 513 through 514 removed outlier: 3.523A pdb=" N ALA B 513 " --> pdb=" O GLY B 767 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 767 " --> pdb=" O ALA B 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.143A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 536 " --> pdb=" O LYS B 762 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.996A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 437 Processing sheet with id=AB3, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AB4, first strand: chain 'C' and resid 737 through 738 removed outlier: 4.125A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 755 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB6, first strand: chain 'D' and resid 514 through 518 removed outlier: 7.821A pdb=" N ALA D 515 " --> pdb=" O GLY D 767 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY D 767 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 514 through 518 removed outlier: 7.821A pdb=" N ALA D 515 " --> pdb=" O GLY D 767 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY D 767 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 538 through 541 Processing sheet with id=AB9, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.531A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 179 through 180 removed outlier: 3.758A pdb=" N CYS E 207 " --> pdb=" O MET E 274 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET E 274 " --> pdb=" O CYS E 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 271 " --> pdb=" O TYR E 242 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL E 239 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP E 243 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU E 251 " --> pdb=" O ASP E 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.682A pdb=" N GLY E 186 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG E 286 " --> pdb=" O LEU E 224 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3646 1.33 - 1.45: 3238 1.45 - 1.57: 8623 1.57 - 1.69: 0 1.69 - 1.81: 157 Bond restraints: 15664 Sorted by residual: bond pdb=" N PRO E 325 " pdb=" CA PRO E 325 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.48e+01 bond pdb=" N THR E 301 " pdb=" CA THR E 301 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" CA ALA E 323 " pdb=" CB ALA E 323 " ideal model delta sigma weight residual 1.528 1.486 0.043 1.56e-02 4.11e+03 7.54e+00 bond pdb=" N CYS E 297 " pdb=" CA CYS E 297 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.27e-02 6.20e+03 6.56e+00 bond pdb=" N PHE E 302 " pdb=" CA PHE E 302 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.54e+00 ... (remaining 15659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 20274 1.78 - 3.55: 749 3.55 - 5.33: 131 5.33 - 7.10: 34 7.10 - 8.88: 10 Bond angle restraints: 21198 Sorted by residual: angle pdb=" N VAL E 293 " pdb=" CA VAL E 293 " pdb=" C VAL E 293 " ideal model delta sigma weight residual 111.58 104.64 6.94 1.06e+00 8.90e-01 4.28e+01 angle pdb=" N ASN D 751 " pdb=" CA ASN D 751 " pdb=" C ASN D 751 " ideal model delta sigma weight residual 114.16 105.77 8.39 1.48e+00 4.57e-01 3.21e+01 angle pdb=" C LEU C 556 " pdb=" N ASN C 557 " pdb=" CA ASN C 557 " ideal model delta sigma weight residual 119.78 125.72 -5.94 1.24e+00 6.50e-01 2.30e+01 angle pdb=" CA PRO E 325 " pdb=" C PRO E 325 " pdb=" O PRO E 325 " ideal model delta sigma weight residual 121.34 115.91 5.43 1.14e+00 7.69e-01 2.27e+01 angle pdb=" C PRO E 325 " pdb=" CA PRO E 325 " pdb=" CB PRO E 325 " ideal model delta sigma weight residual 111.46 105.61 5.85 1.29e+00 6.01e-01 2.06e+01 ... (remaining 21193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 8700 21.82 - 43.63: 651 43.63 - 65.45: 68 65.45 - 87.26: 39 87.26 - 109.08: 29 Dihedral angle restraints: 9487 sinusoidal: 3944 harmonic: 5543 Sorted by residual: dihedral pdb=" CB CYS E 316 " pdb=" SG CYS E 316 " pdb=" SG CYS E 331 " pdb=" CB CYS E 331 " ideal model delta sinusoidal sigma weight residual -86.00 -158.69 72.69 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CA ASN E 311 " pdb=" C ASN E 311 " pdb=" N ASN E 312 " pdb=" CA ASN E 312 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ARG E 284 " pdb=" C ARG E 284 " pdb=" N PHE E 285 " pdb=" CA PHE E 285 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 9484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2268 0.093 - 0.186: 119 0.186 - 0.279: 10 0.279 - 0.372: 1 0.372 - 0.465: 2 Chirality restraints: 2400 Sorted by residual: chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA TYR E 324 " pdb=" N TYR E 324 " pdb=" C TYR E 324 " pdb=" CB TYR E 324 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 2397 not shown) Planarity restraints: 2667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 292 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C PHE E 292 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE E 292 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 293 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 451 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO B 452 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 613 " 0.019 2.00e-02 2.50e+03 1.36e-02 4.65e+00 pdb=" CG TRP C 613 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 613 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 613 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 613 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 613 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 613 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 613 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 613 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 613 " 0.005 2.00e-02 2.50e+03 ... (remaining 2664 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 321 2.67 - 3.23: 15702 3.23 - 3.78: 23166 3.78 - 4.34: 30140 4.34 - 4.90: 47787 Nonbonded interactions: 117116 Sorted by model distance: nonbonded pdb=" O GLY D 489 " pdb=" NH1 ARG D 523 " model vdw 2.110 3.120 nonbonded pdb=" O LEU B 674 " pdb=" OH TYR B 682 " model vdw 2.117 3.040 nonbonded pdb=" O LEU A 674 " pdb=" OH TYR A 682 " model vdw 2.153 3.040 nonbonded pdb=" O ASN C 596 " pdb=" OD1 ASN C 596 " model vdw 2.211 3.040 nonbonded pdb=" O TRP A 798 " pdb=" ND2 ASN A 802 " model vdw 2.213 3.120 ... (remaining 117111 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 431 through 527 or (resid 528 and (name N or name CA or na \ me C or name O or name CB )) or resid 529 through 663 or (resid 664 and (name N \ or name CA or name C or name O or name CB )) or resid 665 through 850)) selection = (chain 'B' and (resid 431 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 691 or (resid 692 and (name N \ or name CA or name C or name O or name CB )) or resid 693 through 850)) selection = (chain 'C' and (resid 431 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 663 or (resid \ 664 and (name N or name CA or name C or name O or name CB )) or resid 665 throug \ h 691 or (resid 692 and (name N or name CA or name C or name O or name CB )) or \ resid 693 through 850)) selection = (chain 'D' and (resid 431 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 691 or (resid \ 692 and (name N or name CA or name C or name O or name CB )) or resid 693 throug \ h 850)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.004 0.052 15681 Z= 0.213 Angle : 0.849 14.386 21244 Z= 0.464 Chirality : 0.050 0.465 2400 Planarity : 0.004 0.055 2659 Dihedral : 16.744 109.077 5916 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.75 % Favored : 91.20 % Rotamer: Outliers : 0.18 % Allowed : 0.30 % Favored : 99.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1909 helix: 0.61 (0.18), residues: 827 sheet: -1.47 (0.53), residues: 100 loop : -2.99 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 775 TYR 0.028 0.002 TYR E 324 PHE 0.022 0.002 PHE C 642 TRP 0.036 0.002 TRP C 613 HIS 0.007 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00417 (15664) covalent geometry : angle 0.81834 (21198) SS BOND : bond 0.01105 ( 5) SS BOND : angle 1.93971 ( 10) hydrogen bonds : bond 0.13806 ( 664) hydrogen bonds : angle 6.20942 ( 1947) link_BETA1-4 : bond 0.01227 ( 4) link_BETA1-4 : angle 3.60245 ( 12) link_NAG-ASN : bond 0.00916 ( 8) link_NAG-ASN : angle 6.22877 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9040 (m) cc_final: 0.8784 (p) REVERT: A 610 ASN cc_start: 0.8241 (t0) cc_final: 0.8022 (t0) REVERT: A 633 THR cc_start: 0.8852 (p) cc_final: 0.8462 (m) REVERT: A 794 MET cc_start: 0.8210 (mpp) cc_final: 0.7929 (mpp) REVERT: A 867 MET cc_start: 0.4852 (pmm) cc_final: 0.3214 (mmm) REVERT: B 568 LEU cc_start: 0.8514 (mm) cc_final: 0.8263 (mt) REVERT: B 705 MET cc_start: 0.7415 (mtm) cc_final: 0.6544 (mpp) REVERT: C 691 MET cc_start: 0.8370 (ttp) cc_final: 0.8161 (ttp) REVERT: C 705 MET cc_start: 0.8836 (mmm) cc_final: 0.8204 (mmm) REVERT: D 478 TYR cc_start: 0.6613 (m-10) cc_final: 0.6350 (m-10) REVERT: D 588 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 632 SER cc_start: 0.9030 (m) cc_final: 0.8721 (m) REVERT: E 243 ASP cc_start: 0.7071 (p0) cc_final: 0.6693 (p0) REVERT: E 324 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6973 (m-80) outliers start: 3 outliers final: 0 residues processed: 247 average time/residue: 0.0982 time to fit residues: 38.9744 Evaluate side-chains 193 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 596 ASN D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099141 restraints weight = 34521.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098605 restraints weight = 30055.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099682 restraints weight = 28172.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.101108 restraints weight = 20085.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101321 restraints weight = 17827.829| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15681 Z= 0.150 Angle : 0.734 13.246 21244 Z= 0.365 Chirality : 0.046 0.426 2400 Planarity : 0.004 0.059 2659 Dihedral : 11.393 85.077 2326 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.21 % Allowed : 9.00 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1909 helix: 0.93 (0.18), residues: 836 sheet: -1.96 (0.44), residues: 133 loop : -3.00 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 748 TYR 0.018 0.001 TYR C 844 PHE 0.026 0.002 PHE D 555 TRP 0.026 0.001 TRP C 613 HIS 0.003 0.001 HIS C 508 Details of bonding type rmsd covalent geometry : bond 0.00335 (15664) covalent geometry : angle 0.70226 (21198) SS BOND : bond 0.00470 ( 5) SS BOND : angle 2.56487 ( 10) hydrogen bonds : bond 0.04637 ( 664) hydrogen bonds : angle 4.95050 ( 1947) link_BETA1-4 : bond 0.01188 ( 4) link_BETA1-4 : angle 3.22993 ( 12) link_NAG-ASN : bond 0.00900 ( 8) link_NAG-ASN : angle 5.72982 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8381 (ptp) REVERT: A 575 SER cc_start: 0.9090 (m) cc_final: 0.8824 (p) REVERT: A 610 ASN cc_start: 0.8095 (t0) cc_final: 0.7879 (t0) REVERT: A 705 MET cc_start: 0.9003 (mtm) cc_final: 0.8370 (ptp) REVERT: A 709 MET cc_start: 0.8149 (mpp) cc_final: 0.7820 (mpp) REVERT: A 867 MET cc_start: 0.4847 (pmm) cc_final: 0.3364 (mmm) REVERT: B 603 GLU cc_start: 0.4117 (mm-30) cc_final: 0.3663 (mm-30) REVERT: C 712 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7548 (mmp80) REVERT: D 478 TYR cc_start: 0.6753 (m-10) cc_final: 0.6517 (m-10) REVERT: D 588 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 632 SER cc_start: 0.9071 (m) cc_final: 0.8748 (m) REVERT: E 228 MET cc_start: 0.7418 (mmp) cc_final: 0.5851 (ptt) REVERT: E 324 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6557 (m-80) outliers start: 20 outliers final: 11 residues processed: 221 average time/residue: 0.0943 time to fit residues: 33.2967 Evaluate side-chains 198 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 353 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 30 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 133 optimal weight: 0.0170 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092409 restraints weight = 35308.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094811 restraints weight = 22601.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096321 restraints weight = 17560.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097191 restraints weight = 15340.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097497 restraints weight = 14204.458| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15681 Z= 0.169 Angle : 0.712 13.214 21244 Z= 0.353 Chirality : 0.046 0.449 2400 Planarity : 0.004 0.056 2659 Dihedral : 9.117 71.349 2326 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 1.99 % Allowed : 13.22 % Favored : 84.78 % 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 are not related in a simple way. whole: -1.55 (0.19), residues: 1909 helix: 0.97 (0.18), residues: 829 sheet: -1.81 (0.44), residues: 133 loop : -2.92 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 543 TYR 0.022 0.001 TYR C 682 PHE 0.028 0.002 PHE D 555 TRP 0.022 0.002 TRP C 613 HIS 0.003 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00390 (15664) covalent geometry : angle 0.68144 (21198) SS BOND : bond 0.01075 ( 5) SS BOND : angle 2.20177 ( 10) hydrogen bonds : bond 0.04389 ( 664) hydrogen bonds : angle 4.71088 ( 1947) link_BETA1-4 : bond 0.00922 ( 4) link_BETA1-4 : angle 2.89562 ( 12) link_NAG-ASN : bond 0.00832 ( 8) link_NAG-ASN : angle 5.64835 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8328 (ptp) REVERT: A 575 SER cc_start: 0.9198 (m) cc_final: 0.8900 (p) REVERT: A 620 MET cc_start: 0.8852 (ttm) cc_final: 0.8449 (ttm) REVERT: A 705 MET cc_start: 0.9093 (mtm) cc_final: 0.8273 (ptp) REVERT: A 709 MET cc_start: 0.8095 (mpp) cc_final: 0.7827 (mpp) REVERT: A 788 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: A 867 MET cc_start: 0.5128 (pmm) cc_final: 0.3529 (mmm) REVERT: B 603 GLU cc_start: 0.4005 (mm-30) cc_final: 0.3562 (mm-30) REVERT: C 620 MET cc_start: 0.8797 (mmt) cc_final: 0.8579 (mmt) REVERT: C 682 TYR cc_start: 0.6408 (m-10) cc_final: 0.6192 (m-10) REVERT: D 478 TYR cc_start: 0.6954 (m-10) cc_final: 0.6693 (m-10) REVERT: D 588 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7945 (mm-30) REVERT: D 632 SER cc_start: 0.9073 (m) cc_final: 0.8757 (m) REVERT: E 324 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: E 326 TRP cc_start: 0.8104 (m100) cc_final: 0.7795 (m100) outliers start: 33 outliers final: 20 residues processed: 223 average time/residue: 0.0975 time to fit residues: 35.3413 Evaluate side-chains 212 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 324 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 42 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091931 restraints weight = 35049.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094337 restraints weight = 22489.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095486 restraints weight = 17552.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096627 restraints weight = 15434.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097061 restraints weight = 14215.056| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15681 Z= 0.176 Angle : 0.708 13.314 21244 Z= 0.350 Chirality : 0.046 0.471 2400 Planarity : 0.004 0.057 2659 Dihedral : 7.905 59.992 2326 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.72 % Allowed : 15.16 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 1909 helix: 0.98 (0.18), residues: 836 sheet: -1.75 (0.44), residues: 133 loop : -2.90 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 543 TYR 0.028 0.001 TYR C 733 PHE 0.028 0.002 PHE D 555 TRP 0.021 0.001 TRP C 613 HIS 0.003 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00408 (15664) covalent geometry : angle 0.67947 (21198) SS BOND : bond 0.00592 ( 5) SS BOND : angle 1.77135 ( 10) hydrogen bonds : bond 0.04249 ( 664) hydrogen bonds : angle 4.59881 ( 1947) link_BETA1-4 : bond 0.00922 ( 4) link_BETA1-4 : angle 2.65946 ( 12) link_NAG-ASN : bond 0.00805 ( 8) link_NAG-ASN : angle 5.62181 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8368 (ptp) REVERT: A 575 SER cc_start: 0.9210 (m) cc_final: 0.8891 (p) REVERT: A 709 MET cc_start: 0.8162 (mpp) cc_final: 0.7830 (mpp) REVERT: A 867 MET cc_start: 0.5149 (pmm) cc_final: 0.3493 (mmm) REVERT: B 603 GLU cc_start: 0.4205 (mm-30) cc_final: 0.3850 (mm-30) REVERT: C 620 MET cc_start: 0.8819 (mmt) cc_final: 0.8530 (mmt) REVERT: C 658 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8056 (t80) REVERT: C 793 MET cc_start: 0.8170 (tpp) cc_final: 0.7595 (tpp) REVERT: D 478 TYR cc_start: 0.6986 (m-10) cc_final: 0.6731 (m-10) REVERT: D 588 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7982 (mm-30) REVERT: D 632 SER cc_start: 0.9094 (m) cc_final: 0.8805 (m) REVERT: D 705 MET cc_start: 0.9353 (tpt) cc_final: 0.8991 (tpt) REVERT: E 292 PHE cc_start: 0.7604 (t80) cc_final: 0.7135 (t80) REVERT: E 324 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: E 326 TRP cc_start: 0.8062 (m100) cc_final: 0.7737 (m100) outliers start: 45 outliers final: 27 residues processed: 225 average time/residue: 0.0927 time to fit residues: 34.0575 Evaluate side-chains 209 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 ASN D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090663 restraints weight = 35360.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092887 restraints weight = 22954.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094341 restraints weight = 18127.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095168 restraints weight = 15831.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095564 restraints weight = 14673.669| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15681 Z= 0.206 Angle : 0.729 13.448 21244 Z= 0.359 Chirality : 0.047 0.500 2400 Planarity : 0.004 0.054 2659 Dihedral : 7.462 59.920 2326 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 3.20 % Allowed : 17.27 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1909 helix: 0.94 (0.18), residues: 839 sheet: -1.72 (0.44), residues: 138 loop : -2.93 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 374 TYR 0.019 0.001 TYR C 733 PHE 0.032 0.002 PHE A 533 TRP 0.020 0.002 TRP C 613 HIS 0.004 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00478 (15664) covalent geometry : angle 0.70064 (21198) SS BOND : bond 0.00577 ( 5) SS BOND : angle 1.62728 ( 10) hydrogen bonds : bond 0.04314 ( 664) hydrogen bonds : angle 4.59489 ( 1947) link_BETA1-4 : bond 0.00878 ( 4) link_BETA1-4 : angle 2.40003 ( 12) link_NAG-ASN : bond 0.00777 ( 8) link_NAG-ASN : angle 5.68488 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8374 (ptp) REVERT: A 575 SER cc_start: 0.9211 (m) cc_final: 0.8895 (p) REVERT: A 620 MET cc_start: 0.8803 (mmt) cc_final: 0.8541 (mmt) REVERT: A 633 THR cc_start: 0.9058 (p) cc_final: 0.8839 (m) REVERT: A 709 MET cc_start: 0.8146 (mpp) cc_final: 0.7741 (mpp) REVERT: A 723 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.5968 (pt0) REVERT: B 603 GLU cc_start: 0.4204 (mm-30) cc_final: 0.3898 (mm-30) REVERT: C 620 MET cc_start: 0.8809 (mmt) cc_final: 0.8485 (mmt) REVERT: C 658 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8114 (t80) REVERT: C 705 MET cc_start: 0.9564 (mmm) cc_final: 0.8914 (mmm) REVERT: C 712 ARG cc_start: 0.8146 (mmp80) cc_final: 0.7932 (mmp80) REVERT: C 793 MET cc_start: 0.8208 (tpp) cc_final: 0.7669 (tpp) REVERT: D 588 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8017 (mm-30) REVERT: D 632 SER cc_start: 0.9111 (m) cc_final: 0.8836 (m) REVERT: E 292 PHE cc_start: 0.7395 (t80) cc_final: 0.6808 (t80) REVERT: E 366 ILE cc_start: 0.8991 (tp) cc_final: 0.8757 (tp) outliers start: 53 outliers final: 36 residues processed: 230 average time/residue: 0.0924 time to fit residues: 34.4548 Evaluate side-chains 227 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 127 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096318 restraints weight = 35108.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096482 restraints weight = 22515.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097393 restraints weight = 22608.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097558 restraints weight = 17533.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097798 restraints weight = 16832.498| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15681 Z= 0.164 Angle : 0.697 13.605 21244 Z= 0.343 Chirality : 0.046 0.512 2400 Planarity : 0.004 0.055 2659 Dihedral : 7.049 59.918 2324 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.08 % Allowed : 18.30 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1909 helix: 1.03 (0.18), residues: 843 sheet: -1.78 (0.43), residues: 150 loop : -2.83 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 374 TYR 0.019 0.001 TYR C 733 PHE 0.028 0.002 PHE D 555 TRP 0.022 0.001 TRP C 613 HIS 0.004 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00383 (15664) covalent geometry : angle 0.66737 (21198) SS BOND : bond 0.00530 ( 5) SS BOND : angle 2.41806 ( 10) hydrogen bonds : bond 0.04104 ( 664) hydrogen bonds : angle 4.45095 ( 1947) link_BETA1-4 : bond 0.00946 ( 4) link_BETA1-4 : angle 2.30123 ( 12) link_NAG-ASN : bond 0.00818 ( 8) link_NAG-ASN : angle 5.63942 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8421 (ptp) REVERT: A 575 SER cc_start: 0.9192 (m) cc_final: 0.8890 (p) REVERT: A 620 MET cc_start: 0.8757 (mmt) cc_final: 0.8548 (mmm) REVERT: A 705 MET cc_start: 0.8996 (mtm) cc_final: 0.8205 (ptp) REVERT: A 709 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7725 (mpp) REVERT: A 723 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.5974 (pt0) REVERT: A 867 MET cc_start: 0.5086 (pmm) cc_final: 0.3531 (tpt) REVERT: B 603 GLU cc_start: 0.4039 (mm-30) cc_final: 0.3823 (mm-30) REVERT: B 691 MET cc_start: 0.7387 (ptt) cc_final: 0.7170 (ptt) REVERT: C 620 MET cc_start: 0.8765 (mmt) cc_final: 0.8454 (mmt) REVERT: C 658 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8112 (t80) REVERT: C 705 MET cc_start: 0.9531 (mmm) cc_final: 0.8829 (mmm) REVERT: C 793 MET cc_start: 0.8172 (tpp) cc_final: 0.7611 (tpp) REVERT: D 478 TYR cc_start: 0.7108 (m-10) cc_final: 0.6836 (m-10) REVERT: D 584 PHE cc_start: 0.7075 (m-10) cc_final: 0.6432 (t80) REVERT: D 588 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7956 (tm-30) REVERT: D 632 SER cc_start: 0.9121 (m) cc_final: 0.8844 (m) REVERT: D 705 MET cc_start: 0.9342 (tpt) cc_final: 0.8955 (mmm) REVERT: E 292 PHE cc_start: 0.7462 (t80) cc_final: 0.7005 (t80) outliers start: 51 outliers final: 36 residues processed: 238 average time/residue: 0.0973 time to fit residues: 37.2422 Evaluate side-chains 232 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 476 PHE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 140 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 189 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 chunk 92 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100434 restraints weight = 35347.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100088 restraints weight = 35322.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101416 restraints weight = 27469.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102427 restraints weight = 21315.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.102678 restraints weight = 19415.884| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15681 Z= 0.117 Angle : 0.666 13.476 21244 Z= 0.322 Chirality : 0.045 0.525 2400 Planarity : 0.004 0.055 2659 Dihedral : 6.534 59.634 2324 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.54 % Allowed : 19.38 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1909 helix: 1.27 (0.18), residues: 840 sheet: -1.55 (0.44), residues: 139 loop : -2.72 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 543 TYR 0.014 0.001 TYR C 733 PHE 0.023 0.001 PHE D 555 TRP 0.026 0.001 TRP C 613 HIS 0.003 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00264 (15664) covalent geometry : angle 0.63732 (21198) SS BOND : bond 0.00467 ( 5) SS BOND : angle 2.05551 ( 10) hydrogen bonds : bond 0.03706 ( 664) hydrogen bonds : angle 4.21237 ( 1947) link_BETA1-4 : bond 0.00884 ( 4) link_BETA1-4 : angle 2.33591 ( 12) link_NAG-ASN : bond 0.00922 ( 8) link_NAG-ASN : angle 5.40088 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9042 (m) cc_final: 0.8689 (p) REVERT: A 585 SER cc_start: 0.7611 (p) cc_final: 0.7194 (m) REVERT: A 604 ASN cc_start: 0.3346 (OUTLIER) cc_final: 0.3051 (t0) REVERT: A 620 MET cc_start: 0.8753 (mmt) cc_final: 0.8451 (mmm) REVERT: A 705 MET cc_start: 0.8970 (mtm) cc_final: 0.8121 (ptp) REVERT: A 709 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7627 (mpp) REVERT: A 867 MET cc_start: 0.4811 (pmm) cc_final: 0.3171 (tpt) REVERT: B 691 MET cc_start: 0.7500 (ptt) cc_final: 0.7293 (ptt) REVERT: B 833 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 441 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7560 (mt-10) REVERT: C 705 MET cc_start: 0.9496 (mmm) cc_final: 0.8896 (mmm) REVERT: C 712 ARG cc_start: 0.8021 (mmp80) cc_final: 0.7295 (mmm160) REVERT: C 793 MET cc_start: 0.8099 (tpp) cc_final: 0.7501 (tpp) REVERT: D 478 TYR cc_start: 0.7031 (m-10) cc_final: 0.6825 (m-10) REVERT: D 584 PHE cc_start: 0.6855 (m-10) cc_final: 0.6183 (t80) REVERT: D 588 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7940 (tm-30) REVERT: D 632 SER cc_start: 0.9079 (m) cc_final: 0.8766 (m) REVERT: D 705 MET cc_start: 0.9338 (tpt) cc_final: 0.8855 (mmm) REVERT: E 292 PHE cc_start: 0.7322 (t80) cc_final: 0.6802 (t80) outliers start: 42 outliers final: 20 residues processed: 241 average time/residue: 0.0942 time to fit residues: 36.8203 Evaluate side-chains 217 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 274 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 162 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 0.0770 chunk 123 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.131010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099171 restraints weight = 35732.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099005 restraints weight = 24401.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099653 restraints weight = 21672.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100040 restraints weight = 18797.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100288 restraints weight = 17785.926| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15681 Z= 0.123 Angle : 0.674 13.442 21244 Z= 0.328 Chirality : 0.045 0.532 2400 Planarity : 0.004 0.057 2659 Dihedral : 6.358 59.867 2324 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.17 % Allowed : 20.59 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1909 helix: 1.37 (0.18), residues: 837 sheet: -1.51 (0.44), residues: 145 loop : -2.66 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 468 TYR 0.017 0.001 TYR C 733 PHE 0.022 0.001 PHE D 555 TRP 0.023 0.001 TRP C 613 HIS 0.002 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00284 (15664) covalent geometry : angle 0.64651 (21198) SS BOND : bond 0.00478 ( 5) SS BOND : angle 1.90611 ( 10) hydrogen bonds : bond 0.03649 ( 664) hydrogen bonds : angle 4.17009 ( 1947) link_BETA1-4 : bond 0.00739 ( 4) link_BETA1-4 : angle 2.30031 ( 12) link_NAG-ASN : bond 0.00873 ( 8) link_NAG-ASN : angle 5.36413 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7732 (mmt) cc_final: 0.7232 (mmt) REVERT: A 575 SER cc_start: 0.9149 (m) cc_final: 0.8834 (p) REVERT: A 585 SER cc_start: 0.7551 (p) cc_final: 0.7117 (m) REVERT: A 705 MET cc_start: 0.9008 (mtm) cc_final: 0.8186 (ptp) REVERT: A 709 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: A 723 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5894 (pt0) REVERT: A 867 MET cc_start: 0.4811 (pmm) cc_final: 0.3150 (tpt) REVERT: B 536 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8600 (pp) REVERT: B 691 MET cc_start: 0.7590 (ptt) cc_final: 0.7365 (ptt) REVERT: C 441 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7644 (mt-10) REVERT: C 705 MET cc_start: 0.9501 (mmm) cc_final: 0.8846 (mmm) REVERT: C 712 ARG cc_start: 0.8012 (mmp80) cc_final: 0.7262 (mmm160) REVERT: C 793 MET cc_start: 0.8174 (tpp) cc_final: 0.7569 (tpp) REVERT: C 843 LEU cc_start: 0.8918 (mt) cc_final: 0.8682 (mm) REVERT: D 584 PHE cc_start: 0.6944 (m-10) cc_final: 0.6132 (t80) REVERT: D 588 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7935 (tm-30) REVERT: D 631 LEU cc_start: 0.9009 (pp) cc_final: 0.8806 (pp) REVERT: D 632 SER cc_start: 0.9082 (m) cc_final: 0.8788 (m) REVERT: D 658 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: D 705 MET cc_start: 0.9313 (tpt) cc_final: 0.8838 (mmm) REVERT: E 292 PHE cc_start: 0.7239 (t80) cc_final: 0.6744 (t80) REVERT: E 329 ASN cc_start: 0.5376 (OUTLIER) cc_final: 0.4610 (p0) outliers start: 36 outliers final: 23 residues processed: 226 average time/residue: 0.0936 time to fit residues: 34.5820 Evaluate side-chains 218 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 55 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 168 optimal weight: 0.0770 chunk 135 optimal weight: 10.0000 chunk 148 optimal weight: 0.0770 chunk 153 optimal weight: 0.2980 chunk 143 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 overall best weight: 0.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN C 747 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.132568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097552 restraints weight = 34576.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100208 restraints weight = 21398.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101894 restraints weight = 16410.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102765 restraints weight = 14121.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103398 restraints weight = 13032.938| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15681 Z= 0.114 Angle : 0.662 13.167 21244 Z= 0.321 Chirality : 0.044 0.522 2400 Planarity : 0.004 0.058 2659 Dihedral : 5.961 59.547 2324 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.81 % Allowed : 20.89 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1909 helix: 1.42 (0.18), residues: 841 sheet: -1.16 (0.46), residues: 133 loop : -2.59 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 468 TYR 0.015 0.001 TYR C 462 PHE 0.023 0.001 PHE A 612 TRP 0.025 0.001 TRP C 613 HIS 0.001 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00255 (15664) covalent geometry : angle 0.63651 (21198) SS BOND : bond 0.00317 ( 5) SS BOND : angle 1.62953 ( 10) hydrogen bonds : bond 0.03408 ( 664) hydrogen bonds : angle 4.08153 ( 1947) link_BETA1-4 : bond 0.00839 ( 4) link_BETA1-4 : angle 2.33610 ( 12) link_NAG-ASN : bond 0.00908 ( 8) link_NAG-ASN : angle 5.13582 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9101 (m) cc_final: 0.8715 (p) REVERT: A 585 SER cc_start: 0.7471 (p) cc_final: 0.7086 (m) REVERT: A 705 MET cc_start: 0.8994 (mtm) cc_final: 0.8264 (ptp) REVERT: A 709 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7340 (mpp) REVERT: A 723 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5625 (pt0) REVERT: A 867 MET cc_start: 0.4639 (pmm) cc_final: 0.2918 (tpt) REVERT: B 536 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 566 TYR cc_start: 0.7622 (m-80) cc_final: 0.7338 (m-80) REVERT: B 620 MET cc_start: 0.9041 (mpp) cc_final: 0.8537 (mmt) REVERT: B 691 MET cc_start: 0.7593 (ptt) cc_final: 0.7349 (ptt) REVERT: B 833 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8433 (tt) REVERT: C 705 MET cc_start: 0.9445 (mmm) cc_final: 0.8692 (mmm) REVERT: C 712 ARG cc_start: 0.7915 (mmp80) cc_final: 0.7080 (mmm160) REVERT: C 713 ARG cc_start: 0.8064 (tpt170) cc_final: 0.7754 (tpp-160) REVERT: C 793 MET cc_start: 0.8171 (tpp) cc_final: 0.7478 (tpp) REVERT: C 843 LEU cc_start: 0.8916 (mt) cc_final: 0.8685 (mm) REVERT: C 861 MET cc_start: 0.7272 (mmm) cc_final: 0.6587 (tmm) REVERT: D 705 MET cc_start: 0.9276 (tpt) cc_final: 0.8782 (mmm) REVERT: E 180 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8812 (mm-30) REVERT: E 292 PHE cc_start: 0.7124 (t80) cc_final: 0.6601 (t80) REVERT: E 329 ASN cc_start: 0.5105 (OUTLIER) cc_final: 0.4785 (p0) outliers start: 30 outliers final: 17 residues processed: 244 average time/residue: 0.0941 time to fit residues: 37.0008 Evaluate side-chains 224 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 169 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.131737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100447 restraints weight = 35733.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100361 restraints weight = 24421.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101582 restraints weight = 20896.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101786 restraints weight = 17773.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.102029 restraints weight = 17635.949| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15681 Z= 0.129 Angle : 0.682 13.189 21244 Z= 0.330 Chirality : 0.045 0.534 2400 Planarity : 0.004 0.058 2659 Dihedral : 5.909 59.773 2324 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.69 % Allowed : 21.92 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1909 helix: 1.48 (0.18), residues: 837 sheet: -0.75 (0.49), residues: 118 loop : -2.58 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 468 TYR 0.015 0.001 TYR C 462 PHE 0.023 0.002 PHE C 836 TRP 0.024 0.001 TRP A 589 HIS 0.004 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00300 (15664) covalent geometry : angle 0.65723 (21198) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.47389 ( 10) hydrogen bonds : bond 0.03494 ( 664) hydrogen bonds : angle 4.12365 ( 1947) link_BETA1-4 : bond 0.00743 ( 4) link_BETA1-4 : angle 2.19894 ( 12) link_NAG-ASN : bond 0.00837 ( 8) link_NAG-ASN : angle 5.14688 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.8841 (mmt) cc_final: 0.8535 (mmt) REVERT: A 709 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7340 (mpp) REVERT: A 723 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5597 (pt0) REVERT: A 808 GLU cc_start: 0.6919 (mt-10) cc_final: 0.5615 (tt0) REVERT: A 867 MET cc_start: 0.4771 (pmm) cc_final: 0.3117 (mmm) REVERT: B 536 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8647 (pp) REVERT: B 566 TYR cc_start: 0.7816 (m-80) cc_final: 0.7576 (m-80) REVERT: B 691 MET cc_start: 0.7601 (ptt) cc_final: 0.7363 (ptt) REVERT: B 833 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8488 (tt) REVERT: C 705 MET cc_start: 0.9474 (mmm) cc_final: 0.8849 (mmm) REVERT: C 712 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7162 (mmm160) REVERT: C 713 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7791 (tpp-160) REVERT: C 793 MET cc_start: 0.8145 (tpp) cc_final: 0.7512 (tpp) REVERT: D 705 MET cc_start: 0.9318 (tpt) cc_final: 0.8828 (mmm) REVERT: D 794 MET cc_start: 0.8855 (ttm) cc_final: 0.8330 (ttm) REVERT: E 243 ASP cc_start: 0.6710 (p0) cc_final: 0.6251 (p0) REVERT: E 292 PHE cc_start: 0.7146 (t80) cc_final: 0.6749 (t80) REVERT: E 329 ASN cc_start: 0.5259 (OUTLIER) cc_final: 0.4802 (p0) REVERT: E 369 GLN cc_start: 0.8653 (pm20) cc_final: 0.8028 (tt0) outliers start: 28 outliers final: 21 residues processed: 225 average time/residue: 0.0967 time to fit residues: 35.1089 Evaluate side-chains 217 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 102 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 68 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 89 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 192 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102198 restraints weight = 34858.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103525 restraints weight = 28750.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104930 restraints weight = 21338.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105793 restraints weight = 17301.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106167 restraints weight = 16512.920| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15681 Z= 0.119 Angle : 0.683 13.072 21244 Z= 0.330 Chirality : 0.044 0.524 2400 Planarity : 0.004 0.058 2659 Dihedral : 5.816 59.640 2324 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.63 % Allowed : 23.01 % Favored : 75.36 % 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 are not related in a simple way. whole: -0.83 (0.20), residues: 1909 helix: 1.46 (0.18), residues: 839 sheet: -1.14 (0.45), residues: 136 loop : -2.51 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 468 TYR 0.019 0.001 TYR B 844 PHE 0.019 0.001 PHE D 555 TRP 0.022 0.001 TRP C 613 HIS 0.002 0.000 HIS C 792 Details of bonding type rmsd covalent geometry : bond 0.00273 (15664) covalent geometry : angle 0.65966 (21198) SS BOND : bond 0.00433 ( 5) SS BOND : angle 1.49365 ( 10) hydrogen bonds : bond 0.03434 ( 664) hydrogen bonds : angle 4.08842 ( 1947) link_BETA1-4 : bond 0.00816 ( 4) link_BETA1-4 : angle 2.20037 ( 12) link_NAG-ASN : bond 0.00853 ( 8) link_NAG-ASN : angle 5.06802 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.93 seconds wall clock time: 40 minutes 21.19 seconds (2421.19 seconds total)