Starting phenix.real_space_refine on Fri Jul 3 19:02:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f5b_31464/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f5b_31464/07_2026/7f5b_31464.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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: 20 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: 3.06, per 1000 atoms: 0.20 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: 0.91 Conformation dependent library (CDL) restraints added in 705.2 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: 0.67 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: 2.49 Time building geometry restraints manager: 1.20 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 - 17.94: 8257 17.94 - 35.88: 823 35.88 - 53.82: 127 53.82 - 71.76: 19 71.76 - 89.70: 13 Dihedral angle restraints: 9239 sinusoidal: 3696 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 9236 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: 1.230 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.580 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 14.292 89.698 5668 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/Z covalent geometry : bond 0.00417 / 0.21 (15664) covalent geometry : angle 0.81834 / 0.46 (21198) SS BOND : bond 0.01105 / 0.53 ( 5) SS BOND : angle 1.93971 / 1.33 ( 10) hydrogen bonds : bond 0.13806 / 8.87 ( 664) hydrogen bonds : angle 6.20942 / 4.35 ( 1947) link_BETA1-4 : bond 0.01227 / 0.61 ( 4) link_BETA1-4 : angle 3.60245 / 1.67 ( 12) link_NAG-ASN : bond 0.00916 / 0.44 ( 8) link_NAG-ASN : angle 6.22877 / 4.02 ( 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 : 0.460 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: 0.7930 (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: 0.7962 (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: 0.6987 (m-80) outliers start: 3 outliers final: 0 residues processed: 247 average time/residue: 0.0912 time to fit residues: 36.2338 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 : 0.505 ------------------------------------------------------------------------------- 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... 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099611 restraints weight = 34945.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098681 restraints weight = 32162.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099920 restraints weight = 29321.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101413 restraints weight = 21030.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101694 restraints weight = 18675.328| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15681 Z= 0.148 Angle : 0.718 13.673 21244 Z= 0.360 Chirality : 0.046 0.415 2400 Planarity : 0.004 0.058 2659 Dihedral : 5.732 58.623 2078 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.15 % Allowed : 9.00 % Favored : 89.86 % 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: 0.91 (0.18), residues: 830 sheet: -1.97 (0.44), residues: 133 loop : -2.95 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 775 TYR 0.020 0.002 TYR C 682 PHE 0.026 0.002 PHE A 555 TRP 0.026 0.001 TRP C 613 HIS 0.003 0.001 HIS C 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15664) covalent geometry : angle 0.68725 / 0.35 (21198) SS BOND : bond 0.00589 / 0.29 ( 5) SS BOND : angle 2.69656 / 1.79 ( 10) hydrogen bonds : bond 0.04680 / 3.14 ( 664) hydrogen bonds : angle 4.93237 / 3.43 ( 1947) link_BETA1-4 : bond 0.01069 / 0.53 ( 4) link_BETA1-4 : angle 2.98171 / 1.39 ( 12) link_NAG-ASN : bond 0.00988 / 0.47 ( 8) link_NAG-ASN : angle 5.67658 / 3.65 ( 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 232 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8386 (ptp) REVERT: A 575 SER cc_start: 0.9087 (m) cc_final: 0.8821 (p) REVERT: A 610 ASN cc_start: 0.8106 (t0) cc_final: 0.7885 (t0) REVERT: A 705 MET cc_start: 0.9014 (mtm) cc_final: 0.8392 (ptp) REVERT: A 709 MET cc_start: 0.8147 (mpp) cc_final: 0.7753 (mpp) REVERT: A 867 MET cc_start: 0.4827 (pmm) cc_final: 0.3382 (mmm) REVERT: B 603 GLU cc_start: 0.4291 (mm-30) cc_final: 0.3835 (mm-30) REVERT: C 712 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7541 (mmp80) REVERT: D 478 TYR cc_start: 0.6750 (m-10) cc_final: 0.6510 (m-10) REVERT: D 588 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7996 (mm-30) REVERT: D 632 SER cc_start: 0.9075 (m) cc_final: 0.8749 (m) REVERT: E 228 MET cc_start: 0.7433 (mmp) cc_final: 0.5870 (ptt) REVERT: E 324 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6573 (m-80) outliers start: 19 outliers final: 10 residues processed: 220 average time/residue: 0.0895 time to fit residues: 31.6861 Evaluate side-chains 195 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3800 r_free = 0.3800 target = 0.125624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090469 restraints weight = 35283.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092773 restraints weight = 23966.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092939 restraints weight = 17554.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093072 restraints weight = 17252.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093199 restraints weight = 17581.057| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15681 Z= 0.252 Angle : 0.761 13.758 21244 Z= 0.384 Chirality : 0.047 0.437 2400 Planarity : 0.004 0.056 2659 Dihedral : 5.918 59.494 2078 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.29 % Allowed : 13.47 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.19), residues: 1909 helix: 0.81 (0.18), residues: 829 sheet: -1.77 (0.44), residues: 136 loop : -2.98 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 727 TYR 0.026 0.002 TYR C 682 PHE 0.037 0.002 PHE A 533 TRP 0.022 0.002 TRP C 613 HIS 0.004 0.001 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (15664) covalent geometry : angle 0.73228 / 0.38 (21198) SS BOND : bond 0.00651 / 0.31 ( 5) SS BOND : angle 2.45883 / 1.65 ( 10) hydrogen bonds : bond 0.04736 / 3.16 ( 664) hydrogen bonds : angle 4.94165 / 3.45 ( 1947) link_BETA1-4 : bond 0.01014 / 0.51 ( 4) link_BETA1-4 : angle 2.87933 / 1.32 ( 12) link_NAG-ASN : bond 0.00770 / 0.38 ( 8) link_NAG-ASN : angle 5.69333 / 3.68 ( 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 235 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8392 (ptp) REVERT: A 575 SER cc_start: 0.9226 (m) cc_final: 0.8943 (p) REVERT: A 610 ASN cc_start: 0.8150 (t0) cc_final: 0.7930 (t0) REVERT: A 709 MET cc_start: 0.8227 (mpp) cc_final: 0.7868 (mpp) REVERT: A 718 VAL cc_start: 0.7756 (t) cc_final: 0.7553 (t) REVERT: C 620 MET cc_start: 0.8871 (mmt) cc_final: 0.8625 (mmt) REVERT: C 712 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7503 (mmp80) REVERT: D 478 TYR cc_start: 0.7084 (m-10) cc_final: 0.6758 (m-10) REVERT: D 584 PHE cc_start: 0.7034 (m-10) cc_final: 0.6463 (t80) REVERT: D 588 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8159 (mm-30) REVERT: D 632 SER cc_start: 0.9103 (m) cc_final: 0.8824 (m) REVERT: D 705 MET cc_start: 0.9359 (mmm) cc_final: 0.9141 (tpt) REVERT: E 309 CYS cc_start: 0.6005 (m) cc_final: 0.4951 (m) REVERT: E 324 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6731 (m-80) outliers start: 38 outliers final: 29 residues processed: 218 average time/residue: 0.0812 time to fit residues: 28.9024 Evaluate side-chains 220 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 737 MET 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 504 GLU 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 C residue 831 LEU 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 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 Chi-restraints excluded: chain E residue 353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 42 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099266 restraints weight = 35140.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099205 restraints weight = 31132.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100076 restraints weight = 31494.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101159 restraints weight = 21341.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101734 restraints weight = 18936.633| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15681 Z= 0.129 Angle : 0.668 13.055 21244 Z= 0.331 Chirality : 0.045 0.406 2400 Planarity : 0.004 0.057 2659 Dihedral : 5.569 59.229 2078 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.36 % Allowed : 15.52 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.45 (0.20), residues: 1909 helix: 1.04 (0.18), residues: 836 sheet: -1.86 (0.45), residues: 129 loop : -2.85 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 543 TYR 0.022 0.001 TYR C 733 PHE 0.027 0.002 PHE D 555 TRP 0.023 0.001 TRP C 613 HIS 0.003 0.000 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15664) covalent geometry : angle 0.63920 / 0.32 (21198) SS BOND : bond 0.00816 / 0.40 ( 5) SS BOND : angle 1.87593 / 1.51 ( 10) hydrogen bonds : bond 0.04085 / 2.76 ( 664) hydrogen bonds : angle 4.54282 / 3.17 ( 1947) link_BETA1-4 : bond 0.01069 / 0.53 ( 4) link_BETA1-4 : angle 2.68684 / 1.23 ( 12) link_NAG-ASN : bond 0.00896 / 0.43 ( 8) link_NAG-ASN : angle 5.37558 / 3.49 ( 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 244 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8410 (ptp) REVERT: A 575 SER cc_start: 0.9056 (m) cc_final: 0.8733 (p) REVERT: A 705 MET cc_start: 0.9084 (mtm) cc_final: 0.8251 (ptp) REVERT: A 709 MET cc_start: 0.8095 (mpp) cc_final: 0.7715 (mpp) REVERT: A 788 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: A 867 MET cc_start: 0.5063 (pmm) cc_final: 0.3606 (tpt) REVERT: B 529 PHE cc_start: 0.8672 (m-10) cc_final: 0.8385 (m-80) REVERT: B 603 GLU cc_start: 0.3978 (mm-30) cc_final: 0.3617 (mm-30) REVERT: C 590 TYR cc_start: 0.7297 (t80) cc_final: 0.6847 (t80) REVERT: C 620 MET cc_start: 0.8726 (mmt) cc_final: 0.8467 (mmt) REVERT: C 793 MET cc_start: 0.8032 (tpp) cc_final: 0.7446 (tpp) REVERT: D 588 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 632 SER cc_start: 0.9056 (m) cc_final: 0.8749 (m) REVERT: D 705 MET cc_start: 0.9310 (mmm) cc_final: 0.8990 (tpt) REVERT: E 292 PHE cc_start: 0.7587 (t80) cc_final: 0.7116 (t80) REVERT: E 324 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: E 326 TRP cc_start: 0.8051 (m100) cc_final: 0.7706 (m100) outliers start: 39 outliers final: 15 residues processed: 226 average time/residue: 0.0805 time to fit residues: 29.4610 Evaluate side-chains 205 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 760 ASP Chi-restraints excluded: chain A residue 788 GLU 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 571 CYS 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 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 324 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 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: 4.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3831 r_free = 0.3831 target = 0.127795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098042 restraints weight = 35722.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099337 restraints weight = 31026.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100359 restraints weight = 23539.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100872 restraints weight = 19311.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.102234 restraints weight = 18346.061| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15681 Z= 0.182 Angle : 0.703 13.048 21244 Z= 0.349 Chirality : 0.046 0.420 2400 Planarity : 0.004 0.054 2659 Dihedral : 5.579 57.913 2078 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.48 % Allowed : 17.27 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1909 helix: 1.02 (0.18), residues: 839 sheet: -1.74 (0.44), residues: 138 loop : -2.88 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 374 TYR 0.021 0.001 TYR C 733 PHE 0.038 0.002 PHE D 579 TRP 0.022 0.001 TRP C 613 HIS 0.004 0.001 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (15664) covalent geometry : angle 0.67557 / 0.34 (21198) SS BOND : bond 0.00754 / 0.37 ( 5) SS BOND : angle 1.80354 / 1.45 ( 10) hydrogen bonds : bond 0.04200 / 2.82 ( 664) hydrogen bonds : angle 4.54708 / 3.19 ( 1947) link_BETA1-4 : bond 0.00993 / 0.49 ( 4) link_BETA1-4 : angle 2.63032 / 1.20 ( 12) link_NAG-ASN : bond 0.00793 / 0.39 ( 8) link_NAG-ASN : angle 5.38532 / 3.49 ( 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 238 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8434 (ptp) REVERT: A 575 SER cc_start: 0.9099 (m) cc_final: 0.8767 (p) REVERT: A 620 MET cc_start: 0.8689 (mmm) cc_final: 0.8488 (ttm) REVERT: A 709 MET cc_start: 0.8090 (mpp) cc_final: 0.7707 (mpp) REVERT: A 723 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5811 (pt0) REVERT: A 788 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: A 867 MET cc_start: 0.5149 (pmm) cc_final: 0.3603 (tpt) REVERT: B 529 PHE cc_start: 0.8701 (m-10) cc_final: 0.8404 (m-80) REVERT: B 603 GLU cc_start: 0.3918 (mm-30) cc_final: 0.3640 (mm-30) REVERT: B 861 MET cc_start: 0.4910 (ttp) cc_final: 0.4701 (ttp) REVERT: C 793 MET cc_start: 0.8109 (tpp) cc_final: 0.7562 (tpp) REVERT: D 588 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7990 (tm-30) REVERT: D 632 SER cc_start: 0.9109 (m) cc_final: 0.8817 (m) REVERT: D 705 MET cc_start: 0.9276 (mmm) cc_final: 0.8743 (tpt) REVERT: E 292 PHE cc_start: 0.7362 (t80) cc_final: 0.6852 (t80) outliers start: 41 outliers final: 30 residues processed: 222 average time/residue: 0.0860 time to fit residues: 30.9168 Evaluate side-chains 217 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 674 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 788 GLU 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 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 571 CYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 611 SER 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 435 VAL 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 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: 8.9990 chunk 59 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 ASN ** 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 591 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093569 restraints weight = 34998.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096096 restraints weight = 21925.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097626 restraints weight = 16929.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098312 restraints weight = 14678.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099057 restraints weight = 13637.041| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15681 Z= 0.137 Angle : 0.664 12.640 21244 Z= 0.328 Chirality : 0.044 0.402 2400 Planarity : 0.004 0.055 2659 Dihedral : 5.255 30.307 2076 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.72 % Allowed : 18.06 % Favored : 79.23 % 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: -1.28 (0.20), residues: 1909 helix: 1.20 (0.18), residues: 836 sheet: -1.65 (0.45), residues: 133 loop : -2.81 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 543 TYR 0.017 0.001 TYR C 733 PHE 0.026 0.001 PHE D 555 TRP 0.023 0.001 TRP C 613 HIS 0.004 0.001 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15664) covalent geometry : angle 0.63754 / 0.32 (21198) SS BOND : bond 0.00530 / 0.26 ( 5) SS BOND : angle 1.63169 / 1.30 ( 10) hydrogen bonds : bond 0.03902 / 2.64 ( 664) hydrogen bonds : angle 4.35674 / 3.05 ( 1947) link_BETA1-4 : bond 0.00992 / 0.49 ( 4) link_BETA1-4 : angle 2.54187 / 1.15 ( 12) link_NAG-ASN : bond 0.00845 / 0.42 ( 8) link_NAG-ASN : angle 5.23023 / 3.40 ( 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 251 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8342 (ptp) REVERT: A 575 SER cc_start: 0.9190 (m) cc_final: 0.8878 (p) REVERT: A 620 MET cc_start: 0.8636 (mmm) cc_final: 0.8282 (ttm) REVERT: A 705 MET cc_start: 0.9058 (mtm) cc_final: 0.8201 (ptp) REVERT: A 709 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7644 (mpp) REVERT: A 788 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: A 867 MET cc_start: 0.5086 (pmm) cc_final: 0.3660 (tpt) REVERT: B 529 PHE cc_start: 0.8784 (m-10) cc_final: 0.8401 (m-80) REVERT: B 603 GLU cc_start: 0.3830 (mm-30) cc_final: 0.3624 (mm-30) REVERT: B 626 LEU cc_start: 0.8818 (mt) cc_final: 0.8585 (mp) REVERT: B 691 MET cc_start: 0.7354 (ptt) cc_final: 0.7135 (ptt) REVERT: C 658 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8131 (t80) REVERT: C 793 MET cc_start: 0.8175 (tpp) cc_final: 0.7568 (tpp) REVERT: D 584 PHE cc_start: 0.6963 (m-10) cc_final: 0.6298 (t80) REVERT: D 588 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7936 (tm-30) REVERT: D 632 SER cc_start: 0.9107 (m) cc_final: 0.8806 (m) REVERT: D 705 MET cc_start: 0.9212 (mmm) cc_final: 0.8590 (tpt) REVERT: E 292 PHE cc_start: 0.7354 (t80) cc_final: 0.6886 (t80) REVERT: E 326 TRP cc_start: 0.8031 (m100) cc_final: 0.7696 (m100) outliers start: 45 outliers final: 27 residues processed: 238 average time/residue: 0.0848 time to fit residues: 32.9935 Evaluate side-chains 217 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 534 MET Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 788 GLU 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 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 501 MET Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 571 CYS 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 435 VAL 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 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: 0.9990 chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 92 optimal weight: 7.9990 chunk 155 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 604 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3863 r_free = 0.3863 target = 0.130087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100661 restraints weight = 34199.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101701 restraints weight = 29669.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103035 restraints weight = 22468.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103551 restraints weight = 18003.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105423 restraints weight = 17145.470| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2180 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= 0.132 Angle : 0.669 12.400 21244 Z= 0.329 Chirality : 0.045 0.397 2400 Planarity : 0.004 0.055 2659 Dihedral : 5.163 31.532 2076 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.78 % Allowed : 19.57 % Favored : 77.66 % 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: -1.18 (0.20), residues: 1909 helix: 1.26 (0.18), residues: 836 sheet: -1.65 (0.43), residues: 145 loop : -2.73 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 634 TYR 0.015 0.001 TYR C 733 PHE 0.024 0.001 PHE D 555 TRP 0.022 0.001 TRP C 613 HIS 0.003 0.000 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15664) covalent geometry : angle 0.64153 / 0.32 (21198) SS BOND : bond 0.00525 / 0.25 ( 5) SS BOND : angle 2.57538 / 1.63 ( 10) hydrogen bonds : bond 0.03803 / 2.57 ( 664) hydrogen bonds : angle 4.27217 / 3.00 ( 1947) link_BETA1-4 : bond 0.00947 / 0.47 ( 4) link_BETA1-4 : angle 2.48096 / 1.13 ( 12) link_NAG-ASN : bond 0.00849 / 0.42 ( 8) link_NAG-ASN : angle 5.13597 / 3.34 ( 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 244 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9056 (m) cc_final: 0.8720 (p) REVERT: A 620 MET cc_start: 0.8604 (mmm) cc_final: 0.8139 (ttm) REVERT: A 627 MET cc_start: 0.7294 (mmm) cc_final: 0.7041 (mtt) REVERT: A 705 MET cc_start: 0.9126 (mtm) cc_final: 0.8169 (ptp) REVERT: A 709 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7622 (mpp) REVERT: A 723 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5752 (pt0) REVERT: A 788 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: A 867 MET cc_start: 0.5097 (pmm) cc_final: 0.3529 (tpt) REVERT: B 529 PHE cc_start: 0.8690 (m-80) cc_final: 0.8344 (m-80) REVERT: B 626 LEU cc_start: 0.8782 (mt) cc_final: 0.8543 (mp) REVERT: B 691 MET cc_start: 0.7377 (ptt) cc_final: 0.7156 (ptt) REVERT: B 833 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8673 (tt) REVERT: C 441 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7494 (mt-10) REVERT: C 658 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8160 (t80) REVERT: C 705 MET cc_start: 0.9476 (mmm) cc_final: 0.9148 (mmm) REVERT: C 712 ARG cc_start: 0.8024 (mmp80) cc_final: 0.7315 (mmm160) REVERT: C 793 MET cc_start: 0.8097 (tpp) cc_final: 0.7533 (tpp) REVERT: D 584 PHE cc_start: 0.6901 (m-10) cc_final: 0.6229 (t80) REVERT: D 588 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7896 (tm-30) REVERT: D 632 SER cc_start: 0.9106 (m) cc_final: 0.8784 (m) REVERT: D 705 MET cc_start: 0.9155 (mmm) cc_final: 0.8567 (mmm) REVERT: E 278 GLU cc_start: 0.8474 (pp20) cc_final: 0.8228 (pp20) REVERT: E 292 PHE cc_start: 0.7307 (t80) cc_final: 0.6813 (t80) outliers start: 46 outliers final: 28 residues processed: 227 average time/residue: 0.0871 time to fit residues: 32.0859 Evaluate side-chains 219 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 576 CYS Chi-restraints excluded: chain A residue 577 VAL 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 788 GLU 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 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 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 435 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 162 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 ASN ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.130256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.095728 restraints weight = 35538.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097427 restraints weight = 23894.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098288 restraints weight = 18496.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098951 restraints weight = 15988.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099223 restraints weight = 15636.329| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15681 Z= 0.132 Angle : 0.661 12.156 21244 Z= 0.326 Chirality : 0.044 0.395 2400 Planarity : 0.004 0.057 2659 Dihedral : 5.098 33.439 2076 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.90 % Allowed : 19.63 % Favored : 77.48 % 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: -1.10 (0.20), residues: 1909 helix: 1.31 (0.18), residues: 838 sheet: -1.54 (0.43), residues: 145 loop : -2.68 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.015 0.001 TYR C 733 PHE 0.024 0.001 PHE D 555 TRP 0.022 0.001 TRP C 613 HIS 0.003 0.000 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (15664) covalent geometry : angle 0.63474 / 0.32 (21198) SS BOND : bond 0.00430 / 0.21 ( 5) SS BOND : angle 2.13363 / 1.43 ( 10) hydrogen bonds : bond 0.03733 / 2.52 ( 664) hydrogen bonds : angle 4.21389 / 2.96 ( 1947) link_BETA1-4 : bond 0.00941 / 0.47 ( 4) link_BETA1-4 : angle 2.42011 / 1.10 ( 12) link_NAG-ASN : bond 0.00835 / 0.41 ( 8) link_NAG-ASN : angle 5.04799 / 3.28 ( 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 255 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 SER cc_start: 0.9176 (m) cc_final: 0.8857 (p) REVERT: A 620 MET cc_start: 0.8495 (mmm) cc_final: 0.8105 (ttm) REVERT: A 705 MET cc_start: 0.9165 (mtm) cc_final: 0.8211 (ptp) REVERT: A 709 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7575 (mpp) REVERT: A 723 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5905 (pt0) REVERT: A 788 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: A 867 MET cc_start: 0.5096 (pmm) cc_final: 0.3511 (tpt) REVERT: B 536 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8618 (pp) REVERT: B 691 MET cc_start: 0.7585 (ptt) cc_final: 0.7359 (ptt) REVERT: C 441 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7529 (mt-10) REVERT: C 658 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8142 (t80) REVERT: C 712 ARG cc_start: 0.7985 (mmp80) cc_final: 0.7260 (mmm160) REVERT: C 793 MET cc_start: 0.8164 (tpp) cc_final: 0.7546 (tpp) REVERT: D 584 PHE cc_start: 0.6885 (m-10) cc_final: 0.6149 (t80) REVERT: D 588 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7973 (tm-30) REVERT: D 631 LEU cc_start: 0.9017 (pp) cc_final: 0.8813 (pp) REVERT: D 632 SER cc_start: 0.9107 (m) cc_final: 0.8802 (m) REVERT: D 658 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: D 705 MET cc_start: 0.9126 (mmm) cc_final: 0.8531 (tpt) REVERT: E 180 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8948 (mm-30) REVERT: E 292 PHE cc_start: 0.7312 (t80) cc_final: 0.6774 (t80) outliers start: 48 outliers final: 33 residues processed: 239 average time/residue: 0.0837 time to fit residues: 32.7536 Evaluate side-chains 230 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE 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 552 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 577 VAL 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 788 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 536 LEU 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 501 MET 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 620 MET Chi-restraints excluded: chain C residue 626 LEU 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 435 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 658 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 55 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 135 optimal weight: 0.0570 chunk 148 optimal weight: 6.9990 chunk 153 optimal weight: 0.0270 chunk 143 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3891 r_free = 0.3891 target = 0.132194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097466 restraints weight = 34284.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099152 restraints weight = 22072.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099865 restraints weight = 16952.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100216 restraints weight = 16473.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100510 restraints weight = 15416.636| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2540 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= 0.118 Angle : 0.673 11.765 21244 Z= 0.328 Chirality : 0.044 0.384 2400 Planarity : 0.004 0.058 2659 Dihedral : 4.950 34.033 2076 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.11 % Allowed : 20.77 % Favored : 77.11 % 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: -0.97 (0.20), residues: 1909 helix: 1.37 (0.18), residues: 838 sheet: -1.16 (0.47), residues: 130 loop : -2.62 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.021 0.001 TYR D 478 PHE 0.023 0.001 PHE D 555 TRP 0.024 0.001 TRP C 613 HIS 0.003 0.000 HIS E 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15664) covalent geometry : angle 0.64965 / 0.32 (21198) SS BOND : bond 0.00362 / 0.17 ( 5) SS BOND : angle 1.82598 / 1.34 ( 10) hydrogen bonds : bond 0.03570 / 2.42 ( 664) hydrogen bonds : angle 4.14883 / 2.90 ( 1947) link_BETA1-4 : bond 0.00908 / 0.45 ( 4) link_BETA1-4 : angle 2.37589 / 1.09 ( 12) link_NAG-ASN : bond 0.00873 / 0.43 ( 8) link_NAG-ASN : angle 4.88624 / 3.18 ( 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 243 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8274 (mm) cc_final: 0.7996 (mt) REVERT: A 575 SER cc_start: 0.9175 (m) cc_final: 0.8790 (p) REVERT: A 709 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7495 (mpp) REVERT: A 788 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: A 867 MET cc_start: 0.4899 (pmm) cc_final: 0.3281 (tpt) REVERT: B 536 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8618 (pp) REVERT: B 566 TYR cc_start: 0.7794 (m-80) cc_final: 0.7533 (m-80) REVERT: B 691 MET cc_start: 0.7622 (ptt) cc_final: 0.7377 (ptt) REVERT: B 833 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8602 (mm) REVERT: C 441 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7627 (mt-10) REVERT: C 658 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8174 (t80) REVERT: C 712 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7176 (mmm160) REVERT: C 713 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7778 (tpp-160) REVERT: C 793 MET cc_start: 0.8188 (tpp) cc_final: 0.7528 (tpp) REVERT: D 534 MET cc_start: 0.8955 (ptt) cc_final: 0.8657 (ptt) REVERT: D 588 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8082 (tm-30) REVERT: D 632 SER cc_start: 0.9185 (m) cc_final: 0.8891 (m) REVERT: D 658 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: D 705 MET cc_start: 0.9030 (mmm) cc_final: 0.8414 (tpt) REVERT: E 180 GLU cc_start: 0.9259 (mm-30) cc_final: 0.9029 (mm-30) REVERT: E 292 PHE cc_start: 0.7318 (t80) cc_final: 0.6735 (t80) REVERT: E 329 ASN cc_start: 0.5721 (OUTLIER) cc_final: 0.5246 (p0) outliers start: 35 outliers final: 23 residues processed: 232 average time/residue: 0.0889 time to fit residues: 33.5866 Evaluate side-chains 227 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 552 VAL 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 788 GLU Chi-restraints excluded: chain B residue 536 LEU 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 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 620 MET Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 658 PHE 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 435 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 658 PHE 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 169 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095456 restraints weight = 35436.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098063 restraints weight = 22067.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099648 restraints weight = 17011.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100393 restraints weight = 14738.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100924 restraints weight = 13652.348| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15681 Z= 0.127 Angle : 0.675 11.684 21244 Z= 0.329 Chirality : 0.044 0.388 2400 Planarity : 0.004 0.058 2659 Dihedral : 4.903 34.938 2076 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.23 % Allowed : 21.01 % Favored : 76.75 % 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: -0.90 (0.20), residues: 1909 helix: 1.43 (0.19), residues: 839 sheet: -1.21 (0.45), residues: 136 loop : -2.57 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 374 TYR 0.019 0.001 TYR D 478 PHE 0.023 0.001 PHE A 612 TRP 0.022 0.001 TRP A 589 HIS 0.002 0.000 HIS C 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15664) covalent geometry : angle 0.65225 / 0.32 (21198) SS BOND : bond 0.00472 / 0.23 ( 5) SS BOND : angle 1.75531 / 1.24 ( 10) hydrogen bonds : bond 0.03569 / 2.41 ( 664) hydrogen bonds : angle 4.15287 / 2.90 ( 1947) link_BETA1-4 : bond 0.00882 / 0.44 ( 4) link_BETA1-4 : angle 2.31433 / 1.06 ( 12) link_NAG-ASN : bond 0.00821 / 0.41 ( 8) link_NAG-ASN : angle 4.85143 / 3.16 ( 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 238 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8224 (mm) cc_final: 0.7956 (mt) REVERT: A 575 SER cc_start: 0.9136 (m) cc_final: 0.8769 (p) REVERT: A 705 MET cc_start: 0.8905 (mtm) cc_final: 0.8284 (ptp) REVERT: A 709 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: A 788 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: A 867 MET cc_start: 0.4900 (pmm) cc_final: 0.3300 (tpt) REVERT: B 536 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 566 TYR cc_start: 0.7830 (m-80) cc_final: 0.7576 (m-80) REVERT: B 691 MET cc_start: 0.7652 (ptt) cc_final: 0.7405 (ptt) REVERT: B 833 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 441 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7672 (mt-10) REVERT: C 658 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8221 (t80) REVERT: C 712 ARG cc_start: 0.7967 (mmp80) cc_final: 0.7253 (mmm160) REVERT: C 713 ARG cc_start: 0.8092 (tpt170) cc_final: 0.7756 (tpp-160) REVERT: C 793 MET cc_start: 0.8193 (tpp) cc_final: 0.7517 (tpp) REVERT: D 534 MET cc_start: 0.9038 (ptt) cc_final: 0.8689 (ptt) REVERT: D 588 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8086 (tm-30) REVERT: D 658 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: E 180 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9008 (mm-30) REVERT: E 243 ASP cc_start: 0.6671 (p0) cc_final: 0.6151 (p0) REVERT: E 292 PHE cc_start: 0.7258 (t80) cc_final: 0.6693 (t80) REVERT: E 329 ASN cc_start: 0.5324 (OUTLIER) cc_final: 0.4882 (p0) outliers start: 37 outliers final: 28 residues processed: 226 average time/residue: 0.0913 time to fit residues: 33.8528 Evaluate side-chains 228 residues out of total 1665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 552 VAL 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 788 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 536 LEU 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 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 620 MET Chi-restraints excluded: chain C residue 626 LEU 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 435 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 658 PHE 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: 5.9990 chunk 156 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3868 r_free = 0.3868 target = 0.131903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100722 restraints weight = 35157.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100632 restraints weight = 22468.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101545 restraints weight = 21773.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101916 restraints weight = 16747.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102200 restraints weight = 16182.530| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2690 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= 0.139 Angle : 0.688 15.191 21244 Z= 0.334 Chirality : 0.044 0.393 2400 Planarity : 0.004 0.058 2659 Dihedral : 4.916 36.944 2076 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.42 % Allowed : 21.32 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1909 helix: 1.39 (0.18), residues: 840 sheet: -1.23 (0.45), residues: 136 loop : -2.54 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 374 TYR 0.019 0.001 TYR D 478 PHE 0.022 0.001 PHE D 555 TRP 0.020 0.001 TRP C 613 HIS 0.002 0.000 HIS C 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15664) covalent geometry : angle 0.66577 / 0.33 (21198) SS BOND : bond 0.00451 / 0.22 ( 5) SS BOND : angle 1.59503 / 1.00 ( 10) hydrogen bonds : bond 0.03658 / 2.46 ( 664) hydrogen bonds : angle 4.17309 / 2.91 ( 1947) link_BETA1-4 : bond 0.00866 / 0.43 ( 4) link_BETA1-4 : angle 2.28014 / 1.04 ( 12) link_NAG-ASN : bond 0.00798 / 0.40 ( 8) link_NAG-ASN : angle 4.84836 / 3.15 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.04 seconds wall clock time: 36 minutes 57.09 seconds (2217.09 seconds total)