Starting phenix.real_space_refine on Wed Sep 17 23:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5q_45218/09_2025/9c5q_45218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5q_45218/09_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_45218/09_2025/9c5q_45218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5q_45218/09_2025/9c5q_45218.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5q_45218/09_2025/9c5q_45218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5q_45218/09_2025/9c5q_45218.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12324 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" 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:plan': 2, ' DC:plan2': 2, ' DG:plan': 3, ' DG:plan2': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" 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: {'ARG:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 113 Restraints were copied for chains: B, A Time building chain proxies: 5.22, per 1000 atoms: 0.42 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=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 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: 1.08 Conformation dependent library (CDL) restraints added in 569.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.24 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: 1.95 Time building geometry restraints manager: 1.38 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: 6553 22.93 - 45.87: 798 45.87 - 68.80: 166 68.80 - 91.73: 21 91.73 - 114.66: 2 Dihedral angle restraints: 7540 sinusoidal: 3042 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 A 344 " pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" CA CYS A 350 " ideal model delta sinusoidal sigma weight residual 79.00 3.31 75.69 1 2.00e+01 2.50e-03 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 ... (remaining 7537 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: 2.25 - 2.78: 2592 2.78 - 3.31: 11250 3.31 - 3.84: 18538 3.84 - 4.37: 20706 4.37 - 4.90: 36570 Nonbonded interactions: 89656 Sorted by model distance: 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 nonbonded pdb=" OH TYR A 331 " pdb=" NE2 HIS A 365 " model vdw 2.293 3.120 ... (remaining 89651 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'A' } 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- 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 12574 Z= 0.124 Angle : 0.566 8.786 17120 Z= 0.308 Chirality : 0.037 0.189 2036 Planarity : 0.004 0.080 2074 Dihedral : 19.490 114.664 4610 Min Nonbonded Distance : 2.248 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (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 ARG 0.002 0.000 ARG A 456 TYR 0.009 0.001 TYR A 362 PHE 0.006 0.001 PHE A 161 TRP 0.007 0.001 TRP A 349 HIS 0.003 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00249 (12572) covalent geometry : angle 0.56615 (17116) SS BOND : bond 0.00040 ( 2) SS BOND : angle 1.28495 ( 4) hydrogen bonds : bond 0.30083 ( 438) hydrogen bonds : angle 7.00693 ( 1278) *********************** 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 : 0.473 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: 0.1374 time to fit residues: 24.3244 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 : 0.335 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.2216 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.153114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116212 restraints weight = 20921.170| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.46 r_work: 0.3473 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12574 Z= 0.109 Angle : 0.547 7.717 17120 Z= 0.288 Chirality : 0.038 0.222 2036 Planarity : 0.004 0.062 2074 Dihedral : 13.289 114.573 1924 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.66 % Rotamer: Outliers : 3.07 % Allowed : 32.79 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.21), residues: 1522 helix: -0.03 (0.19), residues: 782 sheet: -0.70 (0.50), residues: 130 loop : -2.34 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 433 TYR 0.008 0.001 TYR C 84 PHE 0.009 0.001 PHE A 787 TRP 0.005 0.001 TRP C 411 HIS 0.003 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00223 (12572) covalent geometry : angle 0.54689 (17116) SS BOND : bond 0.00236 ( 2) SS BOND : angle 1.33339 ( 4) hydrogen bonds : bond 0.04533 ( 438) hydrogen bonds : angle 4.42824 ( 1278) *********************** 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 157 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.457 Fit side-chains REVERT: C 84 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6208 (t80) REVERT: C 351 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6848 (mm-30) REVERT: A 84 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6206 (t80) REVERT: A 295 SER cc_start: 0.7591 (t) cc_final: 0.7387 (t) REVERT: A 351 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6786 (mm-30) outliers start: 38 outliers final: 22 residues processed: 151 average time/residue: 0.1252 time to fit residues: 26.6800 Evaluate side-chains 135 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 351 GLU 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 645 GLU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 725 LEU 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 298 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 351 GLU 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 645 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU 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 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.148510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111035 restraints weight = 21166.618| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.49 r_work: 0.3411 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12574 Z= 0.142 Angle : 0.561 6.137 17120 Z= 0.296 Chirality : 0.039 0.160 2036 Planarity : 0.004 0.055 2074 Dihedral : 13.328 114.002 1920 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.46 % Favored : 90.41 % Rotamer: Outliers : 5.33 % Allowed : 30.37 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.22), residues: 1522 helix: 0.29 (0.19), residues: 780 sheet: -0.90 (0.49), residues: 128 loop : -2.37 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 433 TYR 0.007 0.001 TYR C 113 PHE 0.011 0.001 PHE A 839 TRP 0.005 0.001 TRP C 277 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00336 (12572) covalent geometry : angle 0.56069 (17116) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.35702 ( 4) hydrogen bonds : bond 0.04857 ( 438) hydrogen bonds : angle 4.19802 ( 1278) *********************** 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 175 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 109 time to evaluate : 0.473 Fit side-chains REVERT: C 84 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6968 (t80) REVERT: C 316 MET cc_start: 0.4845 (tpp) cc_final: 0.4586 (tpt) REVERT: C 351 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: A 84 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 316 MET cc_start: 0.4816 (tpp) cc_final: 0.4554 (tpt) REVERT: A 351 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6910 (mm-30) outliers start: 66 outliers final: 40 residues processed: 163 average time/residue: 0.1166 time to fit residues: 27.4146 Evaluate side-chains 141 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 397 LEU Chi-restraints excluded: chain C residue 404 VAL 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 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 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 276 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 344 CYS 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 539 ILE Chi-restraints excluded: chain A residue 552 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 761 MET 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 5 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.150864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113824 restraints weight = 21041.281| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.45 r_work: 0.3453 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12574 Z= 0.103 Angle : 0.532 7.254 17120 Z= 0.274 Chirality : 0.038 0.140 2036 Planarity : 0.004 0.047 2074 Dihedral : 13.304 113.029 1920 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.61 % Favored : 91.26 % Rotamer: Outliers : 3.80 % Allowed : 32.71 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.22), residues: 1522 helix: 0.42 (0.19), residues: 784 sheet: -1.18 (0.48), residues: 124 loop : -2.28 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 433 TYR 0.008 0.001 TYR A 113 PHE 0.006 0.001 PHE A 787 TRP 0.004 0.001 TRP C 673 HIS 0.002 0.000 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00232 (12572) covalent geometry : angle 0.53209 (17116) SS BOND : bond 0.00246 ( 2) SS BOND : angle 1.14504 ( 4) hydrogen bonds : bond 0.03546 ( 438) hydrogen bonds : angle 4.01151 ( 1278) *********************** 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 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.429 Fit side-chains REVERT: C 84 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 316 MET cc_start: 0.4801 (tpp) cc_final: 0.4485 (tpt) REVERT: C 351 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: C 563 MET cc_start: 0.4716 (mtt) cc_final: 0.4422 (mtt) REVERT: A 84 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7061 (t80) REVERT: A 316 MET cc_start: 0.4826 (tpp) cc_final: 0.4484 (tpt) REVERT: A 351 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: A 563 MET cc_start: 0.4737 (mtt) cc_final: 0.4441 (mtt) outliers start: 47 outliers final: 30 residues processed: 139 average time/residue: 0.1047 time to fit residues: 21.7290 Evaluate side-chains 128 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 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 662 THR 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 276 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 344 CYS 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 662 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU 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 64 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS C 646 ASN A 325 HIS A 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.107384 restraints weight = 21309.505| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.51 r_work: 0.3353 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12574 Z= 0.219 Angle : 0.634 7.807 17120 Z= 0.331 Chirality : 0.042 0.154 2036 Planarity : 0.004 0.046 2074 Dihedral : 13.374 112.247 1920 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.50 % Favored : 88.37 % Rotamer: Outliers : 6.14 % Allowed : 31.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.21), residues: 1522 helix: 0.18 (0.19), residues: 768 sheet: -1.18 (0.43), residues: 148 loop : -2.60 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 433 TYR 0.008 0.001 TYR C 283 PHE 0.017 0.002 PHE C 839 TRP 0.009 0.001 TRP C 277 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00537 (12572) covalent geometry : angle 0.63315 (17116) SS BOND : bond 0.00493 ( 2) SS BOND : angle 1.61832 ( 4) hydrogen bonds : bond 0.05639 ( 438) hydrogen bonds : angle 4.33900 ( 1278) *********************** 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 178 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 102 time to evaluate : 0.528 Fit side-chains REVERT: C 84 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7229 (t80) REVERT: C 217 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8517 (mm-30) REVERT: C 351 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: C 429 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6239 (tt0) REVERT: C 563 MET cc_start: 0.5348 (mtt) cc_final: 0.5076 (mtt) REVERT: A 84 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 217 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8525 (mm-30) REVERT: A 351 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: A 563 MET cc_start: 0.5336 (mtt) cc_final: 0.5071 (mtt) outliers start: 76 outliers final: 46 residues processed: 166 average time/residue: 0.1076 time to fit residues: 26.4640 Evaluate side-chains 148 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 276 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 LEU 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 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 619 LEU Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 661 TRP Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 689 VAL 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 C residue 862 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 344 CYS 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 528 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 661 TRP 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 763 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 862 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 151 optimal weight: 0.0010 chunk 111 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS C 646 ASN A 325 HIS A 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.149794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112803 restraints weight = 21197.438| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.47 r_work: 0.3442 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12574 Z= 0.104 Angle : 0.531 5.977 17120 Z= 0.276 Chirality : 0.038 0.140 2036 Planarity : 0.004 0.045 2074 Dihedral : 13.330 111.844 1920 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.48 % Favored : 91.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.22), residues: 1522 helix: 0.30 (0.19), residues: 786 sheet: -1.44 (0.46), residues: 124 loop : -2.38 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.008 0.001 TYR C 113 PHE 0.014 0.001 PHE C 361 TRP 0.004 0.001 TRP C 673 HIS 0.002 0.000 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00231 (12572) covalent geometry : angle 0.53045 (17116) SS BOND : bond 0.00244 ( 2) SS BOND : angle 1.23931 ( 4) hydrogen bonds : bond 0.03488 ( 438) hydrogen bonds : angle 4.03493 ( 1278) *********************** 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 158 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.480 Fit side-chains REVERT: C 84 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7175 (t80) REVERT: C 217 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8486 (mm-30) REVERT: C 351 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: C 429 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6110 (tt0) REVERT: C 550 MET cc_start: 0.6460 (tmm) cc_final: 0.6214 (tmm) REVERT: C 563 MET cc_start: 0.4566 (mtt) cc_final: 0.4287 (mtt) REVERT: A 84 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7147 (t80) REVERT: A 217 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8506 (mm-30) REVERT: A 351 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6678 (mm-30) REVERT: A 550 MET cc_start: 0.6447 (tmm) cc_final: 0.6204 (tmm) REVERT: A 563 MET cc_start: 0.4595 (mtt) cc_final: 0.4323 (mtt) outliers start: 52 outliers final: 36 residues processed: 150 average time/residue: 0.1035 time to fit residues: 23.1213 Evaluate side-chains 140 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 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 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 645 GLU Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 661 TRP 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 A residue 81 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 344 CYS 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 619 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 661 TRP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 6.9990 chunk 54 optimal weight: 0.0870 chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 153 optimal weight: 0.1980 chunk 121 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.149750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112838 restraints weight = 20944.157| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.47 r_work: 0.3430 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12574 Z= 0.104 Angle : 0.534 6.664 17120 Z= 0.275 Chirality : 0.037 0.139 2036 Planarity : 0.004 0.044 2074 Dihedral : 13.246 110.740 1920 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.00 % Favored : 90.87 % Rotamer: Outliers : 4.44 % Allowed : 33.52 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.22), residues: 1522 helix: 0.38 (0.19), residues: 786 sheet: -1.41 (0.47), residues: 124 loop : -2.40 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 433 TYR 0.007 0.001 TYR A 113 PHE 0.016 0.001 PHE C 361 TRP 0.004 0.001 TRP A 661 HIS 0.003 0.000 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00238 (12572) covalent geometry : angle 0.53361 (17116) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.24968 ( 4) hydrogen bonds : bond 0.03460 ( 438) hydrogen bonds : angle 3.93812 ( 1278) *********************** 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 161 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.484 Fit side-chains REVERT: C 84 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7168 (t80) REVERT: C 217 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8518 (mm-30) REVERT: C 351 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6721 (mm-30) REVERT: C 361 PHE cc_start: 0.4146 (OUTLIER) cc_final: 0.3893 (t80) REVERT: C 429 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6161 (tt0) REVERT: C 563 MET cc_start: 0.4746 (mtt) cc_final: 0.4466 (mtt) REVERT: A 84 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7126 (t80) REVERT: A 217 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8536 (mm-30) REVERT: A 351 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: A 563 MET cc_start: 0.4750 (mtt) cc_final: 0.4466 (mtt) outliers start: 55 outliers final: 35 residues processed: 157 average time/residue: 0.0956 time to fit residues: 22.7033 Evaluate side-chains 136 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 276 SER Chi-restraints excluded: chain C residue 296 VAL 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 361 PHE Chi-restraints excluded: chain C residue 397 LEU 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 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 276 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 344 CYS 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 619 LEU 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 63 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.149825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112875 restraints weight = 21030.164| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.48 r_work: 0.3445 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12574 Z= 0.106 Angle : 0.537 6.252 17120 Z= 0.277 Chirality : 0.038 0.169 2036 Planarity : 0.004 0.044 2074 Dihedral : 13.198 109.957 1920 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.33 % Favored : 90.54 % Rotamer: Outliers : 4.60 % Allowed : 33.60 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.22), residues: 1522 helix: 0.46 (0.19), residues: 786 sheet: -1.41 (0.47), residues: 124 loop : -2.42 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 433 TYR 0.007 0.001 TYR A 113 PHE 0.006 0.001 PHE C 361 TRP 0.004 0.001 TRP A 661 HIS 0.003 0.000 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00244 (12572) covalent geometry : angle 0.53689 (17116) SS BOND : bond 0.00226 ( 2) SS BOND : angle 1.20462 ( 4) hydrogen bonds : bond 0.03439 ( 438) hydrogen bonds : angle 3.88391 ( 1278) *********************** 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 158 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 101 time to evaluate : 0.414 Fit side-chains REVERT: C 84 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 351 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: C 429 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6174 (tt0) REVERT: C 563 MET cc_start: 0.4921 (mtt) cc_final: 0.4625 (mtt) REVERT: A 84 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 351 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: A 563 MET cc_start: 0.4862 (mtt) cc_final: 0.4555 (mtt) outliers start: 57 outliers final: 42 residues processed: 149 average time/residue: 0.1132 time to fit residues: 24.8167 Evaluate side-chains 142 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain C residue 276 SER 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 353 LEU Chi-restraints excluded: chain C residue 397 LEU 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 645 GLU 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 276 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 344 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111890 restraints weight = 21042.694| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.46 r_work: 0.3412 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12574 Z= 0.123 Angle : 0.556 6.657 17120 Z= 0.287 Chirality : 0.039 0.182 2036 Planarity : 0.004 0.044 2074 Dihedral : 13.170 109.307 1920 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.40 % Favored : 90.47 % Rotamer: Outliers : 4.68 % Allowed : 33.20 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.22), residues: 1522 helix: 0.46 (0.19), residues: 786 sheet: -1.51 (0.47), residues: 124 loop : -2.43 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 433 TYR 0.009 0.001 TYR A 331 PHE 0.010 0.001 PHE A 839 TRP 0.005 0.001 TRP C 661 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00291 (12572) covalent geometry : angle 0.55552 (17116) SS BOND : bond 0.00283 ( 2) SS BOND : angle 1.24919 ( 4) hydrogen bonds : bond 0.03794 ( 438) hydrogen bonds : angle 3.92480 ( 1278) *********************** 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 157 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 99 time to evaluate : 0.471 Fit side-chains REVERT: C 84 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 351 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: C 429 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6165 (tt0) REVERT: C 563 MET cc_start: 0.4825 (mtt) cc_final: 0.4528 (mtt) REVERT: A 84 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7065 (t80) REVERT: A 351 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: A 563 MET cc_start: 0.4825 (mtt) cc_final: 0.4535 (mtt) outliers start: 58 outliers final: 46 residues processed: 151 average time/residue: 0.1061 time to fit residues: 23.9530 Evaluate side-chains 148 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 353 LEU Chi-restraints excluded: chain C residue 397 LEU 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 662 THR 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 99 CYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 344 CYS 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 539 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 657 MET 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 737 ILE 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 121 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 94 optimal weight: 0.3980 chunk 139 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 0.0270 chunk 87 optimal weight: 0.9980 overall best weight: 0.2436 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.152797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116149 restraints weight = 21015.923| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.50 r_work: 0.3479 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12574 Z= 0.093 Angle : 0.528 5.845 17120 Z= 0.272 Chirality : 0.037 0.165 2036 Planarity : 0.004 0.044 2074 Dihedral : 13.073 107.778 1920 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.08 % Favored : 91.79 % Rotamer: Outliers : 3.88 % Allowed : 33.68 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.22), residues: 1522 helix: 0.56 (0.19), residues: 790 sheet: -1.34 (0.48), residues: 126 loop : -2.34 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 433 TYR 0.011 0.001 TYR C 331 PHE 0.006 0.000 PHE C 361 TRP 0.006 0.001 TRP A 411 HIS 0.004 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.00205 (12572) covalent geometry : angle 0.52730 (17116) SS BOND : bond 0.00134 ( 2) SS BOND : angle 1.10706 ( 4) hydrogen bonds : bond 0.02671 ( 438) hydrogen bonds : angle 3.82522 ( 1278) ********************** 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 152 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 0.441 Fit side-chains REVERT: C 84 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 126 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 563 MET cc_start: 0.4772 (mtt) cc_final: 0.4466 (mtt) REVERT: A 84 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.6996 (t80) REVERT: A 295 SER cc_start: 0.7815 (t) cc_final: 0.7604 (t) REVERT: A 360 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5178 (mp0) REVERT: A 563 MET cc_start: 0.4776 (mtt) cc_final: 0.4470 (mtt) outliers start: 48 outliers final: 32 residues processed: 147 average time/residue: 0.1068 time to fit residues: 23.5339 Evaluate side-chains 132 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 84 TYR Chi-restraints excluded: chain A residue 99 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 317 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 360 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS C 738 ASN A 325 HIS A 803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.146668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109928 restraints weight = 21106.732| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.43 r_work: 0.3378 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12574 Z= 0.172 Angle : 0.605 10.475 17120 Z= 0.313 Chirality : 0.040 0.154 2036 Planarity : 0.004 0.043 2074 Dihedral : 13.116 107.686 1920 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.45 % Favored : 89.42 % Rotamer: Outliers : 3.72 % Allowed : 34.09 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.22), residues: 1522 helix: 0.39 (0.19), residues: 788 sheet: -1.26 (0.44), residues: 140 loop : -2.53 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 433 TYR 0.013 0.001 TYR A 331 PHE 0.015 0.001 PHE A 839 TRP 0.006 0.001 TRP C 277 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00418 (12572) covalent geometry : angle 0.60454 (17116) SS BOND : bond 0.00360 ( 2) SS BOND : angle 1.37257 ( 4) hydrogen bonds : bond 0.04601 ( 438) hydrogen bonds : angle 4.01701 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.81 seconds wall clock time: 52 minutes 20.19 seconds (3140.19 seconds total)