Starting phenix.real_space_refine on Sun Apr 5 17:59:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyq_64622/04_2026/9uyq_64622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyq_64622/04_2026/9uyq_64622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uyq_64622/04_2026/9uyq_64622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyq_64622/04_2026/9uyq_64622.map" model { file = "/net/cci-nas-00/data/ceres_data/9uyq_64622/04_2026/9uyq_64622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyq_64622/04_2026/9uyq_64622.cif" } resolution = 3.27 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= -0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 76 5.16 5 C 7604 2.51 5 N 2056 2.21 5 O 2216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11954 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5957 Classifications: {'peptide': 776} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 732} Chain breaks: 3 Chain: "A" Number of atoms: 5975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5975 Classifications: {'peptide': 778} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 733} Chain breaks: 3 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.89, per 1000 atoms: 0.24 Number of scatterers: 11954 At special positions: 0 Unit cell: (95.824, 99.216, 185.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 2 15.00 O 2216 8.00 N 2056 7.00 C 7604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 744 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 567.6 milliseconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 47.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 101 through 110 removed outlier: 3.763A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 153 through 165 removed outlier: 3.627A pdb=" N MET B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.644A pdb=" N LEU B 181 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 183 " --> pdb=" O GLU B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 183' Processing helix chain 'B' and resid 196 through 211 removed outlier: 4.188A pdb=" N GLN B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.684A pdb=" N ILE B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.767A pdb=" N ASP B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 366 removed outlier: 3.865A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 401 through 423 removed outlier: 3.660A pdb=" N GLN B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.662A pdb=" N THR B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 620 removed outlier: 3.550A pdb=" N ALA B 618 " --> pdb=" O PRO B 614 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 619 " --> pdb=" O ILE B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 643 removed outlier: 4.008A pdb=" N VAL B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 680 removed outlier: 3.581A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 671 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 719 removed outlier: 4.262A pdb=" N ILE B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 709 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 755 removed outlier: 3.962A pdb=" N LEU B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 773 removed outlier: 3.660A pdb=" N LEU B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 798 removed outlier: 3.804A pdb=" N ILE B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.900A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 807 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 836 removed outlier: 3.538A pdb=" N THR B 821 " --> pdb=" O THR B 817 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET B 834 " --> pdb=" O VAL B 830 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 846 removed outlier: 4.040A pdb=" N THR B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 841 " --> pdb=" O VAL B 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 101 through 110 removed outlier: 3.776A pdb=" N LEU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 4.385A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 4.048A pdb=" N VAL A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.676A pdb=" N SER A 182 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 4.098A pdb=" N GLN A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 259 through 268 removed outlier: 3.512A pdb=" N VAL A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.548A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.823A pdb=" N ASP A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.534A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 423 removed outlier: 3.515A pdb=" N ILE A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.555A pdb=" N TYR A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.768A pdb=" N VAL A 598 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 622 through 642 removed outlier: 4.227A pdb=" N VAL A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE A 639 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 680 removed outlier: 3.964A pdb=" N ARG A 654 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLY A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.699A pdb=" N ILE A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 748 through 772 removed outlier: 3.529A pdb=" N ILE A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER A 758 " --> pdb=" O CYS A 754 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 798 removed outlier: 3.696A pdb=" N ILE A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 removed outlier: 4.358A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 836 removed outlier: 4.078A pdb=" N THR A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 removed outlier: 3.965A pdb=" N VAL A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 843 " --> pdb=" O LYS A 839 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.641A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 41 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 40 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 147 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE B 172 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 148 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 251 removed outlier: 7.955A pdb=" N VAL B 216 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 248 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR B 218 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS B 250 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA B 220 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY B 275 " --> pdb=" O TYR B 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 327 through 331 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.614A pdb=" N ILE B 472 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 491 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 450 through 451 removed outlier: 3.608A pdb=" N PHE B 450 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AA7, first strand: chain 'B' and resid 548 through 549 Processing sheet with id=AA8, first strand: chain 'B' and resid 562 through 564 Processing sheet with id=AA9, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.944A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 41 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 148 through 149 removed outlier: 6.207A pdb=" N VAL A 148 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 244 through 251 removed outlier: 7.730A pdb=" N VAL A 216 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ILE A 249 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 218 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 251 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A 275 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 472 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 491 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN A 474 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA A 489 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 450 through 452 removed outlier: 3.827A pdb=" N PHE A 450 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY A 452 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB5, first strand: chain 'A' and resid 547 through 549 Processing sheet with id=AB6, first strand: chain 'A' and resid 562 through 564 Processing sheet with id=AB7, first strand: chain 'A' and resid 576 through 577 removed outlier: 3.978A pdb=" N VAL A 741 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 724 " --> pdb=" O LYS A 743 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1401 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: 1.64 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3914 1.34 - 1.46: 2848 1.46 - 1.58: 5346 1.58 - 1.70: 2 1.70 - 1.82: 110 Bond restraints: 12220 Sorted by residual: bond pdb=" O3P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O1P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O1P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O2P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O2P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.57e+01 ... (remaining 12215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16482 2.25 - 4.50: 121 4.50 - 6.75: 12 6.75 - 9.00: 7 9.00 - 11.25: 1 Bond angle restraints: 16623 Sorted by residual: angle pdb=" CB MET B 268 " pdb=" CG MET B 268 " pdb=" SD MET B 268 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA ASP B 734 " pdb=" CB ASP B 734 " pdb=" CG ASP B 734 " ideal model delta sigma weight residual 112.60 115.82 -3.22 1.00e+00 1.00e+00 1.04e+01 angle pdb=" CB MET A 562 " pdb=" CG MET A 562 " pdb=" SD MET A 562 " ideal model delta sigma weight residual 112.70 121.56 -8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" CB MET A 789 " pdb=" CG MET A 789 " pdb=" SD MET A 789 " ideal model delta sigma weight residual 112.70 120.83 -8.13 3.00e+00 1.11e-01 7.35e+00 angle pdb=" CB SEP A1001 " pdb=" OG SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 110.00 118.06 -8.06 3.00e+00 1.11e-01 7.21e+00 ... (remaining 16618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 6220 17.53 - 35.05: 825 35.05 - 52.58: 229 52.58 - 70.10: 34 70.10 - 87.63: 14 Dihedral angle restraints: 7322 sinusoidal: 2854 harmonic: 4468 Sorted by residual: dihedral pdb=" CB CYS A 650 " pdb=" SG CYS A 650 " pdb=" SG CYS A 744 " pdb=" CB CYS A 744 " ideal model delta sinusoidal sigma weight residual 93.00 174.35 -81.35 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 543 " pdb=" SG CYS A 543 " pdb=" SG CYS A 555 " pdb=" CB CYS A 555 " ideal model delta sinusoidal sigma weight residual -86.00 -25.11 -60.89 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 7319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1244 0.031 - 0.061: 464 0.061 - 0.092: 113 0.092 - 0.122: 70 0.122 - 0.153: 5 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CB VAL B 775 " pdb=" CA VAL B 775 " pdb=" CG1 VAL B 775 " pdb=" CG2 VAL B 775 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA GLU B 736 " pdb=" N GLU B 736 " pdb=" C GLU B 736 " pdb=" CB GLU B 736 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA PRO B 735 " pdb=" N PRO B 735 " pdb=" C PRO B 735 " pdb=" CB PRO B 735 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1893 not shown) Planarity restraints: 2133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 734 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO A 735 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 735 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 735 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 588 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 589 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 565 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO A 566 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.023 5.00e-02 4.00e+02 ... (remaining 2130 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 983 2.74 - 3.28: 11342 3.28 - 3.82: 18390 3.82 - 4.36: 21302 4.36 - 4.90: 38412 Nonbonded interactions: 90429 Sorted by model distance: nonbonded pdb=" O SER A 823 " pdb=" OG SER A 827 " model vdw 2.202 3.040 nonbonded pdb=" O GLU A 736 " pdb=" NH2 ARG A 739 " model vdw 2.263 3.120 nonbonded pdb=" OE2 GLU A 180 " pdb=" OG SER A 228 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP A 551 " pdb=" OG1 THR A 554 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR B 565 " pdb=" O ASN B 567 " model vdw 2.277 3.040 ... (remaining 90424 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 29 through 680 or resid 692 through 1001)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.830 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 12235 Z= 0.150 Angle : 0.482 11.252 16653 Z= 0.236 Chirality : 0.038 0.153 1896 Planarity : 0.004 0.067 2133 Dihedral : 16.860 87.627 4409 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.16 % Allowed : 30.83 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.03 (0.21), residues: 1538 helix: -0.10 (0.20), residues: 630 sheet: -1.20 (0.39), residues: 189 loop : -0.96 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 739 TYR 0.006 0.001 TYR A 342 PHE 0.005 0.001 PHE A 260 TRP 0.007 0.001 TRP A 493 HIS 0.002 0.000 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00311 (12220) covalent geometry : angle 0.48187 (16623) SS BOND : bond 0.00122 ( 15) SS BOND : angle 0.45811 ( 30) hydrogen bonds : bond 0.29785 ( 476) hydrogen bonds : angle 7.83791 ( 1401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.412 Fit side-chains REVERT: B 734 ASP cc_start: 0.7745 (t0) cc_final: 0.7506 (t0) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.0863 time to fit residues: 14.6137 Evaluate side-chains 106 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 0.5980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.177169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112621 restraints weight = 14488.526| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.05 r_work: 0.3024 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12235 Z= 0.127 Angle : 0.515 6.700 16653 Z= 0.268 Chirality : 0.040 0.154 1896 Planarity : 0.004 0.053 2133 Dihedral : 3.857 43.939 1708 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.74 % Allowed : 28.01 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.57 (0.21), residues: 1538 helix: 0.53 (0.20), residues: 658 sheet: -1.05 (0.39), residues: 182 loop : -1.01 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 621 TYR 0.010 0.001 TYR A 225 PHE 0.008 0.001 PHE A 473 TRP 0.008 0.001 TRP A 715 HIS 0.003 0.000 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00240 (12220) covalent geometry : angle 0.51528 (16623) SS BOND : bond 0.00199 ( 15) SS BOND : angle 0.60148 ( 30) hydrogen bonds : bond 0.06401 ( 476) hydrogen bonds : angle 4.76895 ( 1401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7521 (mtp85) REVERT: A 834 MET cc_start: 0.6836 (mtp) cc_final: 0.6473 (mtt) outliers start: 35 outliers final: 18 residues processed: 135 average time/residue: 0.0926 time to fit residues: 19.1625 Evaluate side-chains 124 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 492 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 712 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 78 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137133 restraints weight = 14820.960| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.63 r_work: 0.3111 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12235 Z= 0.145 Angle : 0.508 6.706 16653 Z= 0.258 Chirality : 0.040 0.155 1896 Planarity : 0.004 0.050 2133 Dihedral : 4.046 50.461 1708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.29 % Allowed : 28.33 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.53 (0.21), residues: 1538 helix: 0.73 (0.21), residues: 658 sheet: -1.12 (0.37), residues: 183 loop : -1.14 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 621 TYR 0.010 0.001 TYR A 225 PHE 0.010 0.001 PHE A 473 TRP 0.015 0.001 TRP A 303 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00338 (12220) covalent geometry : angle 0.50714 (16623) SS BOND : bond 0.00312 ( 15) SS BOND : angle 0.68453 ( 30) hydrogen bonds : bond 0.05400 ( 476) hydrogen bonds : angle 4.24455 ( 1401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 734 ASP cc_start: 0.8033 (t0) cc_final: 0.7816 (t0) REVERT: A 72 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8446 (ttt) REVERT: A 439 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7499 (mtp85) outliers start: 42 outliers final: 23 residues processed: 141 average time/residue: 0.0906 time to fit residues: 19.6017 Evaluate side-chains 133 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 827 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126485 restraints weight = 14843.591| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.67 r_work: 0.3022 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 12235 Z= 0.344 Angle : 0.651 9.228 16653 Z= 0.335 Chirality : 0.046 0.162 1896 Planarity : 0.005 0.048 2133 Dihedral : 4.537 33.965 1706 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.93 % Allowed : 27.23 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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 (0.21), residues: 1538 helix: 0.46 (0.20), residues: 667 sheet: -1.52 (0.35), residues: 193 loop : -1.35 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 274 TYR 0.015 0.002 TYR A 225 PHE 0.019 0.002 PHE B 460 TRP 0.024 0.002 TRP B 303 HIS 0.005 0.001 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00858 (12220) covalent geometry : angle 0.64991 (16623) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.08092 ( 30) hydrogen bonds : bond 0.06493 ( 476) hydrogen bonds : angle 4.39244 ( 1401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 103 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7686 (mtp85) REVERT: A 812 LYS cc_start: 0.7995 (tptm) cc_final: 0.7783 (tppp) outliers start: 63 outliers final: 44 residues processed: 157 average time/residue: 0.0876 time to fit residues: 21.5693 Evaluate side-chains 143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 827 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139011 restraints weight = 14699.256| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.54 r_work: 0.3162 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12235 Z= 0.126 Angle : 0.511 8.102 16653 Z= 0.258 Chirality : 0.040 0.155 1896 Planarity : 0.004 0.049 2133 Dihedral : 4.124 34.141 1706 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.21 % Allowed : 28.56 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.65 (0.21), residues: 1538 helix: 0.77 (0.21), residues: 662 sheet: -1.34 (0.35), residues: 191 loop : -1.33 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 739 TYR 0.010 0.001 TYR A 610 PHE 0.008 0.001 PHE B 473 TRP 0.013 0.001 TRP A 303 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00295 (12220) covalent geometry : angle 0.51033 (16623) SS BOND : bond 0.00231 ( 15) SS BOND : angle 0.66826 ( 30) hydrogen bonds : bond 0.04532 ( 476) hydrogen bonds : angle 4.03564 ( 1401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7472 (mtp85) outliers start: 41 outliers final: 30 residues processed: 132 average time/residue: 0.0824 time to fit residues: 17.4316 Evaluate side-chains 126 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 827 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN A 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131894 restraints weight = 14723.355| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.66 r_work: 0.3089 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12235 Z= 0.136 Angle : 0.509 8.941 16653 Z= 0.256 Chirality : 0.040 0.156 1896 Planarity : 0.004 0.049 2133 Dihedral : 4.036 32.827 1706 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.13 % Allowed : 28.64 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.62 (0.21), residues: 1538 helix: 0.79 (0.21), residues: 661 sheet: -1.27 (0.35), residues: 203 loop : -1.31 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 563 TYR 0.008 0.001 TYR A 225 PHE 0.009 0.001 PHE B 279 TRP 0.014 0.001 TRP A 303 HIS 0.003 0.000 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00324 (12220) covalent geometry : angle 0.50822 (16623) SS BOND : bond 0.00197 ( 15) SS BOND : angle 0.67549 ( 30) hydrogen bonds : bond 0.04339 ( 476) hydrogen bonds : angle 3.91897 ( 1401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7541 (mtp85) outliers start: 40 outliers final: 32 residues processed: 135 average time/residue: 0.0904 time to fit residues: 19.2462 Evaluate side-chains 129 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 827 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 96 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111567 restraints weight = 14655.502| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.83 r_work: 0.3014 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12235 Z= 0.118 Angle : 0.495 9.996 16653 Z= 0.248 Chirality : 0.040 0.153 1896 Planarity : 0.004 0.050 2133 Dihedral : 3.933 32.282 1706 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.13 % Allowed : 28.79 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.50 (0.21), residues: 1538 helix: 0.87 (0.21), residues: 662 sheet: -1.17 (0.35), residues: 203 loop : -1.25 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 527 TYR 0.007 0.001 TYR A 215 PHE 0.008 0.001 PHE B 279 TRP 0.013 0.001 TRP A 303 HIS 0.003 0.000 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00278 (12220) covalent geometry : angle 0.49513 (16623) SS BOND : bond 0.00186 ( 15) SS BOND : angle 0.62497 ( 30) hydrogen bonds : bond 0.03967 ( 476) hydrogen bonds : angle 3.78683 ( 1401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7469 (mtp85) outliers start: 40 outliers final: 31 residues processed: 135 average time/residue: 0.0820 time to fit residues: 17.4332 Evaluate side-chains 128 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 827 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131851 restraints weight = 14644.587| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.53 r_work: 0.3119 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12235 Z= 0.145 Angle : 0.512 10.434 16653 Z= 0.257 Chirality : 0.040 0.155 1896 Planarity : 0.004 0.050 2133 Dihedral : 3.995 31.721 1706 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.36 % Allowed : 28.64 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.55 (0.21), residues: 1538 helix: 0.85 (0.21), residues: 663 sheet: -1.17 (0.35), residues: 202 loop : -1.31 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 563 TYR 0.008 0.001 TYR B 475 PHE 0.009 0.001 PHE B 279 TRP 0.016 0.001 TRP A 303 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00352 (12220) covalent geometry : angle 0.51129 (16623) SS BOND : bond 0.00195 ( 15) SS BOND : angle 0.70615 ( 30) hydrogen bonds : bond 0.04221 ( 476) hydrogen bonds : angle 3.81535 ( 1401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 527 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7180 (ptt180) REVERT: A 439 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7469 (mtp85) REVERT: A 746 MET cc_start: 0.7029 (mpt) cc_final: 0.6735 (mpp) outliers start: 43 outliers final: 35 residues processed: 136 average time/residue: 0.0819 time to fit residues: 17.3913 Evaluate side-chains 135 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 527 ARG Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 827 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131056 restraints weight = 14526.428| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.49 r_work: 0.3108 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12235 Z= 0.138 Angle : 0.516 11.441 16653 Z= 0.257 Chirality : 0.040 0.155 1896 Planarity : 0.004 0.049 2133 Dihedral : 4.001 31.902 1706 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.29 % Allowed : 28.56 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.52 (0.21), residues: 1538 helix: 0.87 (0.21), residues: 663 sheet: -1.13 (0.35), residues: 202 loop : -1.30 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.007 0.001 TYR B 475 PHE 0.009 0.001 PHE A 279 TRP 0.015 0.001 TRP A 303 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00333 (12220) covalent geometry : angle 0.51608 (16623) SS BOND : bond 0.00190 ( 15) SS BOND : angle 0.69800 ( 30) hydrogen bonds : bond 0.04144 ( 476) hydrogen bonds : angle 3.79528 ( 1401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 527 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7184 (ptt180) REVERT: A 439 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7468 (mtp85) REVERT: A 746 MET cc_start: 0.7038 (mpt) cc_final: 0.6754 (mpp) outliers start: 42 outliers final: 37 residues processed: 135 average time/residue: 0.0894 time to fit residues: 18.7191 Evaluate side-chains 137 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 527 ARG Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 144 optimal weight: 0.0370 chunk 124 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112486 restraints weight = 14578.520| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.82 r_work: 0.3034 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12235 Z= 0.106 Angle : 0.496 10.865 16653 Z= 0.246 Chirality : 0.040 0.154 1896 Planarity : 0.004 0.050 2133 Dihedral : 3.858 32.149 1706 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.58 % Allowed : 29.19 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.34 (0.21), residues: 1538 helix: 0.99 (0.21), residues: 663 sheet: -1.00 (0.36), residues: 198 loop : -1.19 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 563 TYR 0.008 0.001 TYR B 665 PHE 0.006 0.001 PHE B 460 TRP 0.010 0.001 TRP B 303 HIS 0.003 0.000 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00244 (12220) covalent geometry : angle 0.49588 (16623) SS BOND : bond 0.00185 ( 15) SS BOND : angle 0.61886 ( 30) hydrogen bonds : bond 0.03649 ( 476) hydrogen bonds : angle 3.70129 ( 1401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 527 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7005 (ptt180) REVERT: A 439 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7449 (mtp85) REVERT: A 746 MET cc_start: 0.7102 (mpt) cc_final: 0.6796 (mpp) outliers start: 33 outliers final: 31 residues processed: 128 average time/residue: 0.0916 time to fit residues: 18.1986 Evaluate side-chains 130 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 527 ARG Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 765 CYS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 750 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 66 optimal weight: 0.4980 chunk 114 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111792 restraints weight = 14598.955| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.79 r_work: 0.3010 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12235 Z= 0.117 Angle : 0.505 11.773 16653 Z= 0.250 Chirality : 0.040 0.154 1896 Planarity : 0.004 0.050 2133 Dihedral : 3.870 31.396 1706 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.97 % Allowed : 28.87 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.31 (0.21), residues: 1538 helix: 1.03 (0.21), residues: 665 sheet: -1.01 (0.36), residues: 203 loop : -1.18 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 563 TYR 0.007 0.001 TYR B 665 PHE 0.008 0.001 PHE B 279 TRP 0.013 0.001 TRP A 303 HIS 0.003 0.000 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00278 (12220) covalent geometry : angle 0.50505 (16623) SS BOND : bond 0.00180 ( 15) SS BOND : angle 0.64226 ( 30) hydrogen bonds : bond 0.03808 ( 476) hydrogen bonds : angle 3.68488 ( 1401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.21 seconds wall clock time: 60 minutes 26.12 seconds (3626.12 seconds total)