Starting phenix.real_space_refine on Wed Jul 30 12:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5q_45218/07_2025/9c5q_45218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5q_45218/07_2025/9c5q_45218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2025/9c5q_45218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2025/9c5q_45218.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2025/9c5q_45218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2025/9c5q_45218.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.017 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 28 5.49 5 S 70 5.16 5 C 7818 2.51 5 N 2068 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12324 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 234 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DC:plan2': 2, ' DG:plan': 3, ' DG:plan2': 3, ' DC:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 5928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5928 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 23, 'TRANS': 751} Chain breaks: 6 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 113 Restraints were copied for chains: C, D Time building chain proxies: 13.90, per 1000 atoms: 1.13 Number of scatterers: 12324 At special positions: 0 Unit cell: (148.78, 128.14, 83.42, 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 70 16.00 P 28 15.00 O 2340 8.00 N 2068 7.00 C 7818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 350 " 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: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 54.6% alpha, 4.8% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.616A pdb=" N TRP C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.556A pdb=" N GLY C 88 " --> pdb=" O TYR C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 3.592A pdb=" N ALA C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 136 removed outlier: 4.507A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.832A pdb=" N ASN C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.535A pdb=" N MET C 220 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 222 " --> pdb=" O HIS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 243 removed outlier: 4.286A pdb=" N THR C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.799A pdb=" N VAL C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.551A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU C 332 " --> pdb=" O SER C 328 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 removed outlier: 3.528A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.633A pdb=" N LEU C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 434 removed outlier: 3.695A pdb=" N ILE C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.726A pdb=" N SER C 448 " --> pdb=" O THR C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 501 through 509 Processing helix chain 'C' and resid 528 through 540 removed outlier: 3.917A pdb=" N ILE C 538 " --> pdb=" O ALA C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 removed outlier: 3.502A pdb=" N THR C 552 " --> pdb=" O GLN C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 563 removed outlier: 3.571A pdb=" N SER C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 589 removed outlier: 3.505A pdb=" N TRP C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 589 " --> pdb=" O CYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 627 through 639 removed outlier: 3.778A pdb=" N ALA C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 653 removed outlier: 3.830A pdb=" N LEU C 653 " --> pdb=" O HIS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 removed outlier: 3.611A pdb=" N PHE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 675 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 688 removed outlier: 3.581A pdb=" N ARG C 682 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 684 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 685 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 removed outlier: 3.821A pdb=" N LEU C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 730 removed outlier: 3.509A pdb=" N PHE C 719 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 720 " --> pdb=" O HIS C 716 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 721 " --> pdb=" O LYS C 717 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 727 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 728 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 729 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.612A pdb=" N ASN C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 739 " --> pdb=" O ARG C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 770 removed outlier: 3.613A pdb=" N GLN C 749 " --> pdb=" O ARG C 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 750 " --> pdb=" O GLY C 746 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 756 " --> pdb=" O GLN C 752 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 761 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 781 removed outlier: 3.625A pdb=" N LEU C 776 " --> pdb=" O HIS C 772 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 786 removed outlier: 3.515A pdb=" N LEU C 785 " --> pdb=" O PHE C 781 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 786 " --> pdb=" O GLN C 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 781 through 786' Processing helix chain 'C' and resid 792 through 797 removed outlier: 4.362A pdb=" N LEU C 796 " --> pdb=" O GLU C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 814 removed outlier: 4.246A pdb=" N ARG C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C 809 " --> pdb=" O GLN C 805 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C 813 " --> pdb=" O VAL C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 835 Processing helix chain 'C' and resid 849 through 858 Processing helix chain 'C' and resid 871 through 891 removed outlier: 3.841A pdb=" N ALA C 876 " --> pdb=" O GLU C 872 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 877 " --> pdb=" O ARG C 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.616A pdb=" N TRP A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.556A pdb=" N GLY A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.592A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.508A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.832A pdb=" N ASN A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.535A pdb=" N MET A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 removed outlier: 4.286A pdb=" N THR A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.799A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.550A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.528A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.633A pdb=" N LEU A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.696A pdb=" N ILE A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.727A pdb=" N SER A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 501 through 509 Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.918A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.502A pdb=" N THR A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.571A pdb=" N SER A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.504A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.778A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 removed outlier: 3.830A pdb=" N LEU A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.611A pdb=" N PHE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 675 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.582A pdb=" N ARG A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 removed outlier: 3.821A pdb=" N LEU A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 730 removed outlier: 3.509A pdb=" N PHE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 720 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.612A pdb=" N ASN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.613A pdb=" N GLN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 781 removed outlier: 3.625A pdb=" N LEU A 776 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 removed outlier: 3.515A pdb=" N LEU A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 786 " --> pdb=" O GLN A 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 786' Processing helix chain 'A' and resid 792 through 797 removed outlier: 4.362A pdb=" N LEU A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 814 removed outlier: 4.246A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 849 through 858 Processing helix chain 'A' and resid 871 through 891 removed outlier: 3.841A pdb=" N ALA A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.738A pdb=" N ASP C 169 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 140 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS C 139 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL C 214 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU C 141 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 260 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.676A pdb=" N LYS C 297 " --> pdb=" O CYS C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 439 through 442 removed outlier: 6.471A pdb=" N VAL C 340 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA C 442 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 342 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU C 341 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C 457 " --> pdb=" O ILE C 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 463 through 464 Processing sheet with id=AA5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.738A pdb=" N ASP A 169 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 139 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL A 214 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 141 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 260 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.677A pdb=" N LYS A 297 " --> pdb=" O CYS A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 442 removed outlier: 6.471A pdb=" N VAL A 340 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA A 442 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 342 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 438 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3639 1.34 - 1.46: 1820 1.46 - 1.57: 6947 1.57 - 1.69: 54 1.69 - 1.81: 112 Bond restraints: 12572 Sorted by residual: bond pdb=" CA GLU C 107 " pdb=" CB GLU C 107 " ideal model delta sigma weight residual 1.528 1.548 -0.021 1.39e-02 5.18e+03 2.19e+00 bond pdb=" CA GLU A 107 " pdb=" CB GLU A 107 " ideal model delta sigma weight residual 1.528 1.548 -0.021 1.39e-02 5.18e+03 2.19e+00 bond pdb=" CA LYS C 347 " pdb=" C LYS C 347 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.24e-02 6.50e+03 2.03e+00 bond pdb=" CA LYS A 347 " pdb=" C LYS A 347 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.24e-02 6.50e+03 1.96e+00 bond pdb=" C3' DT D 8 " pdb=" O3' DT D 8 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.71e+00 ... (remaining 12567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 16758 1.76 - 3.51: 307 3.51 - 5.27: 39 5.27 - 7.03: 10 7.03 - 8.79: 2 Bond angle restraints: 17116 Sorted by residual: angle pdb=" N MET C 316 " pdb=" CA MET C 316 " pdb=" C MET C 316 " ideal model delta sigma weight residual 109.31 105.02 4.29 1.42e+00 4.96e-01 9.12e+00 angle pdb=" N MET A 316 " pdb=" CA MET A 316 " pdb=" C MET A 316 " ideal model delta sigma weight residual 109.31 105.02 4.29 1.42e+00 4.96e-01 9.11e+00 angle pdb=" C ILE A 302 " pdb=" CA ILE A 302 " pdb=" CB ILE A 302 " ideal model delta sigma weight residual 111.29 116.18 -4.89 1.64e+00 3.72e-01 8.91e+00 angle pdb=" C ILE C 302 " pdb=" CA ILE C 302 " pdb=" CB ILE C 302 " ideal model delta sigma weight residual 111.29 116.17 -4.88 1.64e+00 3.72e-01 8.85e+00 angle pdb=" CG1 ILE C 302 " pdb=" CB ILE C 302 " pdb=" CG2 ILE C 302 " ideal model delta sigma weight residual 110.70 101.91 8.79 3.00e+00 1.11e-01 8.58e+00 ... (remaining 17111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 6552 22.93 - 45.87: 798 45.87 - 68.80: 165 68.80 - 91.73: 20 91.73 - 114.66: 2 Dihedral angle restraints: 7537 sinusoidal: 3039 harmonic: 4498 Sorted by residual: dihedral pdb=" CA ASN C 337 " pdb=" C ASN C 337 " pdb=" N HIS C 338 " pdb=" CA HIS C 338 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" SG CYS C 344 " pdb=" CB CYS C 350 " pdb=" SG CYS C 350 " pdb=" CA CYS C 350 " ideal model delta sinusoidal sigma weight residual 79.00 3.35 75.65 1 2.00e+01 2.50e-03 1.81e+01 dihedral pdb=" CA ASN A 337 " pdb=" C ASN A 337 " pdb=" N HIS A 338 " pdb=" CA HIS A 338 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 7534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1531 0.038 - 0.076: 398 0.076 - 0.113: 93 0.113 - 0.151: 12 0.151 - 0.189: 2 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CB ILE C 302 " pdb=" CA ILE C 302 " pdb=" CG1 ILE C 302 " pdb=" CG2 ILE C 302 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CB ILE A 302 " pdb=" CA ILE A 302 " pdb=" CG1 ILE A 302 " pdb=" CG2 ILE A 302 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ILE C 302 " pdb=" N ILE C 302 " pdb=" C ILE C 302 " pdb=" CB ILE C 302 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2033 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 624 " 0.052 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO C 625 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 625 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 624 " -0.052 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 625 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 76 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO A 77 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " -0.026 5.00e-02 4.00e+02 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 103 2.61 - 3.18: 10116 3.18 - 3.75: 17732 3.75 - 4.33: 22920 4.33 - 4.90: 38788 Nonbonded interactions: 89659 Sorted by model distance: nonbonded pdb=" SG CYS A 344 " pdb=" SG CYS A 350 " model vdw 2.031 3.760 nonbonded pdb=" OE1 GLU C 217 " pdb=" NE2 HIS C 219 " model vdw 2.248 3.120 nonbonded pdb=" OE1 GLU A 217 " pdb=" NE2 HIS A 219 " model vdw 2.248 3.120 nonbonded pdb=" O SER A 624 " pdb=" OG1 THR A 628 " model vdw 2.248 3.040 nonbonded pdb=" O SER C 624 " pdb=" OG1 THR C 628 " model vdw 2.249 3.040 ... (remaining 89654 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 4.260 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 40.280 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.002 0.050 12573 Z= 0.124 Angle : 0.566 8.786 17118 Z= 0.308 Chirality : 0.037 0.189 2036 Planarity : 0.004 0.080 2074 Dihedral : 19.490 114.664 4610 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 0.65 % Allowed : 35.30 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.21), residues: 1522 helix: -0.60 (0.19), residues: 720 sheet: -0.71 (0.51), residues: 130 loop : -2.24 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 349 HIS 0.003 0.001 HIS C 219 PHE 0.006 0.001 PHE A 161 TYR 0.009 0.001 TYR A 362 ARG 0.002 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.30083 ( 438) hydrogen bonds : angle 7.00693 ( 1278) SS BOND : bond 0.00040 ( 1) SS BOND : angle 1.29737 ( 2) covalent geometry : bond 0.00249 (12572) covalent geometry : angle 0.56615 (17116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.461 Fit side-chains REVERT: C 295 SER cc_start: 0.8397 (t) cc_final: 0.7964 (p) REVERT: C 317 LEU cc_start: 0.6944 (pt) cc_final: 0.6302 (tt) REVERT: A 295 SER cc_start: 0.8358 (t) cc_final: 0.8129 (t) REVERT: A 317 LEU cc_start: 0.6917 (pt) cc_final: 0.6324 (tt) outliers start: 8 outliers final: 4 residues processed: 128 average time/residue: 0.2974 time to fit residues: 53.1855 Evaluate side-chains 112 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 803 ASN Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 803 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN C 325 HIS C 498 ASN C 752 GLN C 767 ASN C 835 ASN A 279 ASN A 325 HIS A 498 ASN A 752 GLN A 767 ASN A 835 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.147435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109982 restraints weight = 21007.894| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.47 r_work: 0.3394 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12573 Z= 0.166 Angle : 0.602 8.118 17118 Z= 0.319 Chirality : 0.040 0.214 2036 Planarity : 0.005 0.064 2074 Dihedral : 13.399 113.811 1924 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.25 % Favored : 89.49 % Rotamer: Outliers : 5.17 % Allowed : 30.94 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1522 helix: -0.16 (0.19), residues: 774 sheet: -0.94 (0.49), residues: 128 loop : -2.45 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 277 HIS 0.005 0.001 HIS A 417 PHE 0.012 0.001 PHE C 839 TYR 0.009 0.001 TYR A 84 ARG 0.004 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05494 ( 438) hydrogen bonds : angle 4.49113 ( 1278) SS BOND : bond 0.00570 ( 1) SS BOND : angle 1.77148 ( 2) covalent geometry : bond 0.00393 (12572) covalent geometry : angle 0.60206 (17116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 113 time to evaluate : 1.378 Fit side-chains REVERT: C 84 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7051 (t80) REVERT: C 351 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: A 84 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7061 (t80) REVERT: A 351 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6980 (mm-30) outliers start: 64 outliers final: 40 residues processed: 167 average time/residue: 0.2632 time to fit residues: 62.6794 Evaluate side-chains 148 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.0270 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 83 optimal weight: 5.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.153180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116394 restraints weight = 21341.244| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.43 r_work: 0.3481 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12573 Z= 0.094 Angle : 0.517 7.469 17118 Z= 0.269 Chirality : 0.037 0.166 2036 Planarity : 0.004 0.053 2074 Dihedral : 13.345 113.194 1920 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.98 % Rotamer: Outliers : 2.91 % Allowed : 33.04 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1522 helix: 0.24 (0.19), residues: 782 sheet: -1.13 (0.48), residues: 126 loop : -2.30 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 411 HIS 0.003 0.000 HIS A 716 PHE 0.006 0.001 PHE C 787 TYR 0.008 0.001 TYR C 113 ARG 0.003 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 438) hydrogen bonds : angle 4.12978 ( 1278) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.20074 ( 2) covalent geometry : bond 0.00201 (12572) covalent geometry : angle 0.51659 (17116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.346 Fit side-chains REVERT: C 84 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7053 (t80) REVERT: C 316 MET cc_start: 0.4849 (tpp) cc_final: 0.4544 (tpt) REVERT: C 351 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: C 563 MET cc_start: 0.4700 (mtt) cc_final: 0.4375 (mtt) REVERT: A 84 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 316 MET cc_start: 0.4850 (tpp) cc_final: 0.4552 (tpt) REVERT: A 351 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6735 (mm-30) REVERT: A 563 MET cc_start: 0.4678 (mtt) cc_final: 0.4365 (mtt) outliers start: 36 outliers final: 24 residues processed: 141 average time/residue: 0.2625 time to fit residues: 52.8330 Evaluate side-chains 127 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 95 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 66 optimal weight: 0.0870 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.152757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115978 restraints weight = 20878.785| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.47 r_work: 0.3468 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12573 Z= 0.093 Angle : 0.516 7.628 17118 Z= 0.265 Chirality : 0.037 0.137 2036 Planarity : 0.004 0.044 2074 Dihedral : 13.234 112.892 1920 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 3.80 % Allowed : 31.99 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1522 helix: 0.52 (0.19), residues: 786 sheet: -1.12 (0.48), residues: 126 loop : -2.30 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 673 HIS 0.002 0.000 HIS A 716 PHE 0.006 0.001 PHE A 787 TYR 0.008 0.001 TYR A 113 ARG 0.004 0.000 ARG C 433 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 438) hydrogen bonds : angle 3.86705 ( 1278) SS BOND : bond 0.00118 ( 1) SS BOND : angle 1.12733 ( 2) covalent geometry : bond 0.00205 (12572) covalent geometry : angle 0.51566 (17116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 1.266 Fit side-chains REVERT: C 84 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6937 (t80) REVERT: C 316 MET cc_start: 0.4899 (tpp) cc_final: 0.4545 (tpt) REVERT: C 351 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6629 (mm-30) REVERT: C 563 MET cc_start: 0.4800 (mtt) cc_final: 0.4484 (mtt) REVERT: A 84 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6932 (t80) REVERT: A 316 MET cc_start: 0.4851 (tpp) cc_final: 0.4440 (tpt) REVERT: A 351 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6751 (mm-30) REVERT: A 563 MET cc_start: 0.4752 (mtt) cc_final: 0.4429 (mtt) outliers start: 47 outliers final: 28 residues processed: 146 average time/residue: 0.2417 time to fit residues: 51.5861 Evaluate side-chains 127 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 56 optimal weight: 0.0770 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114975 restraints weight = 20722.111| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.44 r_work: 0.3458 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12573 Z= 0.096 Angle : 0.510 6.122 17118 Z= 0.263 Chirality : 0.037 0.137 2036 Planarity : 0.004 0.044 2074 Dihedral : 13.181 112.278 1920 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.15 % Favored : 91.72 % Rotamer: Outliers : 4.04 % Allowed : 31.42 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1522 helix: 0.60 (0.19), residues: 780 sheet: -1.20 (0.48), residues: 126 loop : -2.28 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 661 HIS 0.002 0.000 HIS C 417 PHE 0.005 0.001 PHE A 787 TYR 0.007 0.001 TYR C 113 ARG 0.004 0.000 ARG C 433 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 438) hydrogen bonds : angle 3.84478 ( 1278) SS BOND : bond 0.00225 ( 1) SS BOND : angle 1.06472 ( 2) covalent geometry : bond 0.00218 (12572) covalent geometry : angle 0.50954 (17116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 1.391 Fit side-chains REVERT: C 84 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7027 (t80) REVERT: C 316 MET cc_start: 0.4847 (tpp) cc_final: 0.4591 (tmm) REVERT: C 351 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: C 563 MET cc_start: 0.4702 (mtt) cc_final: 0.4396 (mtt) REVERT: A 84 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 316 MET cc_start: 0.4816 (tpp) cc_final: 0.4546 (tmm) REVERT: A 351 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: A 563 MET cc_start: 0.4685 (mtt) cc_final: 0.4382 (mtt) outliers start: 50 outliers final: 36 residues processed: 143 average time/residue: 0.2269 time to fit residues: 48.4573 Evaluate side-chains 133 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 0.0050 chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.152562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115593 restraints weight = 21245.726| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.50 r_work: 0.3466 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12573 Z= 0.091 Angle : 0.511 7.627 17118 Z= 0.262 Chirality : 0.037 0.132 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.129 111.651 1920 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.98 % Rotamer: Outliers : 4.52 % Allowed : 31.58 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1522 helix: 0.62 (0.19), residues: 786 sheet: -1.18 (0.48), residues: 126 loop : -2.24 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 673 HIS 0.002 0.000 HIS C 716 PHE 0.005 0.000 PHE A 787 TYR 0.008 0.001 TYR C 113 ARG 0.005 0.000 ARG C 433 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 438) hydrogen bonds : angle 3.77049 ( 1278) SS BOND : bond 0.00180 ( 1) SS BOND : angle 1.02964 ( 2) covalent geometry : bond 0.00203 (12572) covalent geometry : angle 0.51077 (17116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 1.399 Fit side-chains REVERT: C 84 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7034 (t80) REVERT: C 217 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 316 MET cc_start: 0.4771 (tpp) cc_final: 0.4479 (tmm) REVERT: C 351 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: C 563 MET cc_start: 0.4624 (mtt) cc_final: 0.4324 (mtt) REVERT: A 84 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7025 (t80) REVERT: A 217 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8522 (mm-30) REVERT: A 316 MET cc_start: 0.4776 (tpp) cc_final: 0.4486 (tmm) REVERT: A 351 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: A 563 MET cc_start: 0.4633 (mtt) cc_final: 0.4326 (mtt) outliers start: 56 outliers final: 41 residues processed: 149 average time/residue: 0.2236 time to fit residues: 49.7318 Evaluate side-chains 140 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 137 optimal weight: 0.0170 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.147122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109651 restraints weight = 21210.293| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.49 r_work: 0.3390 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12573 Z= 0.171 Angle : 0.585 7.399 17118 Z= 0.305 Chirality : 0.040 0.151 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.209 111.312 1920 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.38 % Favored : 89.49 % Rotamer: Outliers : 5.01 % Allowed : 32.15 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1522 helix: 0.40 (0.19), residues: 768 sheet: -1.34 (0.47), residues: 124 loop : -2.31 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.005 0.001 HIS C 417 PHE 0.013 0.001 PHE C 839 TYR 0.007 0.001 TYR C 283 ARG 0.005 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 438) hydrogen bonds : angle 4.07785 ( 1278) SS BOND : bond 0.00428 ( 1) SS BOND : angle 1.35512 ( 2) covalent geometry : bond 0.00411 (12572) covalent geometry : angle 0.58476 (17116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 103 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 217 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8571 (mm-30) REVERT: C 316 MET cc_start: 0.5162 (tpp) cc_final: 0.4810 (tmm) REVERT: C 351 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: C 429 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6198 (tt0) REVERT: C 563 MET cc_start: 0.5037 (mtt) cc_final: 0.4761 (mtt) REVERT: A 84 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7193 (t80) REVERT: A 217 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 316 MET cc_start: 0.5048 (tpp) cc_final: 0.4700 (tmm) REVERT: A 351 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: A 563 MET cc_start: 0.4994 (mtt) cc_final: 0.4713 (mtt) outliers start: 62 outliers final: 43 residues processed: 158 average time/residue: 0.2238 time to fit residues: 53.0649 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 114 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 chunk 64 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.150376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113520 restraints weight = 21092.039| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.49 r_work: 0.3446 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12573 Z= 0.099 Angle : 0.528 6.143 17118 Z= 0.273 Chirality : 0.038 0.177 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.165 110.706 1920 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.08 % Favored : 91.79 % Rotamer: Outliers : 4.36 % Allowed : 32.88 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1522 helix: 0.50 (0.19), residues: 782 sheet: -1.22 (0.48), residues: 124 loop : -2.28 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 673 HIS 0.002 0.000 HIS C 417 PHE 0.004 0.001 PHE C 787 TYR 0.007 0.001 TYR C 113 ARG 0.007 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 438) hydrogen bonds : angle 3.89426 ( 1278) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.11957 ( 2) covalent geometry : bond 0.00224 (12572) covalent geometry : angle 0.52821 (17116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7132 (t80) REVERT: C 316 MET cc_start: 0.5047 (tpp) cc_final: 0.4693 (tmm) REVERT: C 351 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: C 360 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5489 (mp0) REVERT: C 429 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6172 (tt0) REVERT: C 563 MET cc_start: 0.4784 (mtt) cc_final: 0.4510 (mtt) REVERT: A 84 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7132 (t80) REVERT: A 217 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8561 (mm-30) REVERT: A 316 MET cc_start: 0.4975 (tpp) cc_final: 0.4603 (tmm) REVERT: A 351 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: A 360 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5479 (mp0) REVERT: A 563 MET cc_start: 0.4755 (mtt) cc_final: 0.4487 (mtt) outliers start: 54 outliers final: 40 residues processed: 154 average time/residue: 0.2604 time to fit residues: 60.3552 Evaluate side-chains 143 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.149456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112589 restraints weight = 20985.410| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.47 r_work: 0.3433 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12573 Z= 0.114 Angle : 0.541 6.576 17118 Z= 0.279 Chirality : 0.038 0.181 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.102 109.895 1920 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.07 % Favored : 90.80 % Rotamer: Outliers : 4.60 % Allowed : 32.55 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1522 helix: 0.54 (0.19), residues: 780 sheet: -1.28 (0.48), residues: 124 loop : -2.30 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 673 HIS 0.003 0.000 HIS C 219 PHE 0.008 0.001 PHE C 839 TYR 0.007 0.001 TYR A 113 ARG 0.006 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 438) hydrogen bonds : angle 3.88899 ( 1278) SS BOND : bond 0.00262 ( 1) SS BOND : angle 1.16563 ( 2) covalent geometry : bond 0.00267 (12572) covalent geometry : angle 0.54067 (17116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7157 (t80) REVERT: C 316 MET cc_start: 0.5080 (tpp) cc_final: 0.4716 (tmm) REVERT: C 351 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6721 (mm-30) REVERT: C 360 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: C 429 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6169 (tt0) REVERT: C 563 MET cc_start: 0.4807 (mtt) cc_final: 0.4535 (mtt) REVERT: A 84 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 316 MET cc_start: 0.5024 (tpp) cc_final: 0.4652 (tmm) REVERT: A 351 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: A 360 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.5474 (mp0) REVERT: A 563 MET cc_start: 0.4806 (mtt) cc_final: 0.4533 (mtt) outliers start: 57 outliers final: 46 residues processed: 148 average time/residue: 0.2362 time to fit residues: 51.6724 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 95 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112416 restraints weight = 21024.908| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.47 r_work: 0.3432 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12573 Z= 0.117 Angle : 0.544 6.525 17118 Z= 0.281 Chirality : 0.038 0.168 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.084 109.191 1920 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.46 % Favored : 90.41 % Rotamer: Outliers : 4.20 % Allowed : 32.96 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1522 helix: 0.54 (0.19), residues: 780 sheet: -1.32 (0.47), residues: 124 loop : -2.30 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 673 HIS 0.004 0.001 HIS A 219 PHE 0.007 0.001 PHE C 839 TYR 0.007 0.001 TYR C 113 ARG 0.007 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 438) hydrogen bonds : angle 3.87794 ( 1278) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.17253 ( 2) covalent geometry : bond 0.00274 (12572) covalent geometry : angle 0.54355 (17116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7148 (t80) REVERT: C 316 MET cc_start: 0.4995 (tpp) cc_final: 0.4618 (tmm) REVERT: C 351 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: C 360 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5337 (mp0) REVERT: C 429 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6174 (tt0) REVERT: C 563 MET cc_start: 0.4879 (mtt) cc_final: 0.4595 (mtt) REVERT: A 84 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7137 (t80) REVERT: A 316 MET cc_start: 0.4959 (tpp) cc_final: 0.4657 (tmm) REVERT: A 351 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6748 (mm-30) REVERT: A 360 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5462 (mp0) REVERT: A 563 MET cc_start: 0.4883 (mtt) cc_final: 0.4598 (mtt) outliers start: 52 outliers final: 46 residues processed: 144 average time/residue: 0.2232 time to fit residues: 47.9848 Evaluate side-chains 149 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 792 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110007 restraints weight = 21128.904| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.45 r_work: 0.3395 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12573 Z= 0.156 Angle : 0.579 6.544 17118 Z= 0.301 Chirality : 0.040 0.161 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.124 108.623 1920 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.71 % Favored : 89.16 % Rotamer: Outliers : 4.44 % Allowed : 32.79 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1522 helix: 0.43 (0.19), residues: 768 sheet: -1.08 (0.44), residues: 140 loop : -2.39 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.005 0.001 HIS C 417 PHE 0.014 0.001 PHE C 839 TYR 0.008 0.001 TYR C 283 ARG 0.006 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 438) hydrogen bonds : angle 4.04337 ( 1278) SS BOND : bond 0.00370 ( 1) SS BOND : angle 1.33527 ( 2) covalent geometry : bond 0.00376 (12572) covalent geometry : angle 0.57913 (17116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6494.00 seconds wall clock time: 112 minutes 16.56 seconds (6736.56 seconds total)