Starting phenix.real_space_refine on Thu Jul 2 20:39:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0a_43706/07_2026/8w0a_43706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0a_43706/07_2026/8w0a_43706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w0a_43706/07_2026/8w0a_43706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0a_43706/07_2026/8w0a_43706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w0a_43706/07_2026/8w0a_43706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0a_43706/07_2026/8w0a_43706.map" } resolution = 3.2 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= 0.012 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 14 5.49 5 S 66 5.16 5 C 6532 2.51 5 N 1708 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10216 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4968 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 616} Chain breaks: 7 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Restraints were copied for chains: A, B Time building chain proxies: 3.86, per 1000 atoms: 0.38 Number of scatterers: 10216 At special positions: 0 Unit cell: (165.98, 93.74, 82.56, 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 66 16.00 P 14 15.00 O 1896 8.00 N 1708 7.00 C 6532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.16 Conformation dependent library (CDL) restraints added in 299.1 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 56.8% alpha, 6.1% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.616A pdb=" N LEU C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 4.008A pdb=" N ALA C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.325A pdb=" N LEU C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 136 removed outlier: 3.907A pdb=" N LEU C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.145A pdb=" N GLU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.628A pdb=" N SER C 183 " --> pdb=" O HIS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.568A pdb=" N LEU C 221 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY C 222 " --> pdb=" O HIS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 244 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.776A pdb=" N VAL C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.734A pdb=" N THR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 removed outlier: 3.512A pdb=" N ASP C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.969A pdb=" N MET C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 4.169A pdb=" N LYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.693A pdb=" N GLU C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 432 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.904A pdb=" N SER C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 528 through 537 removed outlier: 3.538A pdb=" N ARG C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.765A pdb=" N THR C 552 " --> pdb=" O GLN C 548 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 554 " --> pdb=" O MET C 550 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 556 " --> pdb=" O THR C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.823A pdb=" N ALA C 561 " --> pdb=" O THR C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 592 removed outlier: 3.555A pdb=" N TRP C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 589 " --> pdb=" O CYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.839A pdb=" N LEU C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 639 removed outlier: 3.849A pdb=" N LEU C 629 " --> pdb=" O PRO C 625 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 637 " --> pdb=" O ALA C 633 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 653 removed outlier: 3.735A pdb=" N LEU C 653 " --> pdb=" O HIS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 677 through 686 removed outlier: 3.707A pdb=" N ARG C 682 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 730 removed outlier: 3.620A pdb=" N HIS C 716 " --> pdb=" O GLN C 712 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C 719 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 720 " --> pdb=" O HIS C 716 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C 721 " --> pdb=" O LYS C 717 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 725 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 727 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 728 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.798A pdb=" N ILE C 737 " --> pdb=" O PRO C 733 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN C 739 " --> pdb=" O ARG C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 768 removed outlier: 4.206A pdb=" N GLN C 749 " --> pdb=" O ARG C 745 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER C 750 " --> pdb=" O GLY C 746 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 752 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN C 753 " --> pdb=" O GLN C 749 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 761 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 762 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 780 removed outlier: 3.524A pdb=" N GLU C 775 " --> pdb=" O TRP C 771 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 776 " --> pdb=" O HIS C 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 787 removed outlier: 3.740A pdb=" N THR C 786 " --> pdb=" O GLN C 782 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 787 " --> pdb=" O LYS C 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.616A pdb=" N LEU A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 removed outlier: 4.009A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.326A pdb=" N LEU A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 136 removed outlier: 3.908A pdb=" N LEU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.144A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.628A pdb=" N SER A 183 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.568A pdb=" N LEU A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 244 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.776A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.735A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 363 removed outlier: 3.512A pdb=" N ASP A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.970A pdb=" N MET A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 4.169A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.693A pdb=" N GLU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.905A pdb=" N SER A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.538A pdb=" N ARG A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.765A pdb=" N THR A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.823A pdb=" N ALA A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 592 removed outlier: 3.555A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.838A pdb=" N LEU A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.848A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.735A pdb=" N LEU A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 677 through 686 removed outlier: 3.707A pdb=" N ARG A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.620A pdb=" N HIS A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 720 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.797A pdb=" N ILE A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 768 removed outlier: 4.207A pdb=" N GLN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 762 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 removed outlier: 3.524A pdb=" N GLU A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 776 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.740A pdb=" N THR A 786 " --> pdb=" O GLN A 782 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 263 through 264 removed outlier: 6.425A pdb=" N LEU C 111 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN C 110 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR C 283 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 112 " --> pdb=" O TYR C 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.094A pdb=" N PHE C 142 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 214 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 301 through 304 removed outlier: 6.421A pdb=" N VAL C 457 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU C 341 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 414 through 415 removed outlier: 7.444A pdb=" N ALA C 414 " --> pdb=" O ALA C 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 463 through 464 Processing sheet with id=AA6, first strand: chain 'C' and resid 595 through 596 Processing sheet with id=AA7, first strand: chain 'C' and resid 640 through 643 Processing sheet with id=AA8, first strand: chain 'A' and resid 263 through 264 removed outlier: 6.426A pdb=" N LEU A 111 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN A 110 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N TYR A 283 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 112 " --> pdb=" O TYR A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.093A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 214 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 304 removed outlier: 6.421A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 414 through 415 removed outlier: 7.444A pdb=" N ALA A 414 " --> pdb=" O ALA A 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AB4, first strand: chain 'A' and resid 595 through 596 352 hydrogen bonds defined for protein. 1020 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: 1.16 Time building geometry restraints manager: 1.43 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: 3222 1.34 - 1.46: 1698 1.46 - 1.58: 5376 1.58 - 1.70: 26 1.70 - 1.82: 104 Bond restraints: 10426 Sorted by residual: bond pdb=" O3' DT D 4 " pdb=" P DT D 5 " ideal model delta sigma weight residual 1.607 1.584 0.023 1.50e-02 4.44e+03 2.34e+00 bond pdb=" O3' DT B 4 " pdb=" P DT B 5 " ideal model delta sigma weight residual 1.607 1.584 0.023 1.50e-02 4.44e+03 2.34e+00 bond pdb=" O3' DT B 3 " pdb=" P DT B 4 " ideal model delta sigma weight residual 1.607 1.589 0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" O3' DT D 3 " pdb=" P DT D 4 " ideal model delta sigma weight residual 1.607 1.589 0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" C2' DT B 4 " pdb=" C1' DT B 4 " ideal model delta sigma weight residual 1.518 1.529 -0.011 1.00e-02 1.00e+04 1.23e+00 ... (remaining 10421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 13968 1.99 - 3.98: 160 3.98 - 5.97: 18 5.97 - 7.96: 6 7.96 - 9.95: 6 Bond angle restraints: 14158 Sorted by residual: angle pdb=" O4' DT B 6 " pdb=" C4' DT B 6 " pdb=" C3' DT B 6 " ideal model delta sigma weight residual 106.00 104.29 1.71 6.00e-01 2.78e+00 8.09e+00 angle pdb=" CA LEU C 273 " pdb=" CB LEU C 273 " pdb=" CG LEU C 273 " ideal model delta sigma weight residual 116.30 126.25 -9.95 3.50e+00 8.16e-02 8.08e+00 angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 126.23 -9.93 3.50e+00 8.16e-02 8.06e+00 angle pdb=" O4' DT D 6 " pdb=" C4' DT D 6 " pdb=" C3' DT D 6 " ideal model delta sigma weight residual 106.00 104.32 1.68 6.00e-01 2.78e+00 7.87e+00 angle pdb=" O4' DT B 4 " pdb=" C4' DT B 4 " pdb=" C3' DT B 4 " ideal model delta sigma weight residual 106.00 104.35 1.65 6.00e-01 2.78e+00 7.55e+00 ... (remaining 14153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 5019 17.45 - 34.91: 805 34.91 - 52.36: 288 52.36 - 69.81: 62 69.81 - 87.27: 14 Dihedral angle restraints: 6188 sinusoidal: 2516 harmonic: 3672 Sorted by residual: dihedral pdb=" CA PRO A 656 " pdb=" C PRO A 656 " pdb=" N MET A 657 " pdb=" CA MET A 657 " ideal model delta harmonic sigma weight residual 180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO C 656 " pdb=" C PRO C 656 " pdb=" N MET C 657 " pdb=" CA MET C 657 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA MET A 657 " pdb=" C MET A 657 " pdb=" N PHE A 658 " pdb=" CA PHE A 658 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1124 0.035 - 0.070: 408 0.070 - 0.105: 94 0.105 - 0.140: 30 0.140 - 0.175: 4 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CB ILE C 261 " pdb=" CA ILE C 261 " pdb=" CG1 ILE C 261 " pdb=" CG2 ILE C 261 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CB THR C 235 " pdb=" CA THR C 235 " pdb=" OG1 THR C 235 " pdb=" CG2 THR C 235 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 1657 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 781 " 0.007 2.00e-02 2.50e+03 1.48e-02 3.82e+00 pdb=" CG PHE A 781 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 781 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 781 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 781 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 781 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 781 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 781 " 0.007 2.00e-02 2.50e+03 1.47e-02 3.80e+00 pdb=" CG PHE C 781 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 781 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 781 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 781 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 781 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 781 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 279 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ASN A 279 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN A 279 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 280 " 0.008 2.00e-02 2.50e+03 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 4 2.23 - 2.90: 4052 2.90 - 3.56: 14094 3.56 - 4.23: 22123 4.23 - 4.90: 37741 Nonbonded interactions: 78014 Sorted by model distance: nonbonded pdb=" ND2 ASN C 773 " pdb=" O LEU A 644 " model vdw 1.561 3.120 nonbonded pdb=" O LEU C 644 " pdb=" ND2 ASN A 773 " model vdw 1.566 3.120 nonbonded pdb=" CD1 LEU C 776 " pdb=" NE2 GLN A 780 " model vdw 1.935 3.540 nonbonded pdb=" NE2 GLN C 780 " pdb=" CD1 LEU A 776 " model vdw 1.940 3.540 nonbonded pdb=" ND2 ASN A 110 " pdb=" O LEU A 278 " model vdw 2.252 3.120 ... (remaining 78009 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 'C' selection = chain 'A' } ncs_group { reference = chain 'D' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10426 Z= 0.130 Angle : 0.579 9.952 14158 Z= 0.307 Chirality : 0.040 0.175 1660 Planarity : 0.003 0.029 1720 Dihedral : 19.614 87.266 3808 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.09 % Allowed : 36.76 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1240 helix: -0.95 (0.21), residues: 596 sheet: -2.43 (0.66), residues: 68 loop : -1.10 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 480 TYR 0.011 0.001 TYR A 283 PHE 0.032 0.001 PHE A 781 TRP 0.021 0.001 TRP A 277 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (10426) covalent geometry : angle 0.57890 / 0.31 (14158) hydrogen bonds : bond 0.28397 / 19.20 ( 352) hydrogen bonds : angle 7.89477 / 5.52 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 ASP cc_start: 0.3212 (m-30) cc_final: 0.2381 (p0) REVERT: C 538 ILE cc_start: 0.6187 (pt) cc_final: 0.5882 (pt) REVERT: A 402 ASP cc_start: 0.3275 (m-30) cc_final: 0.2469 (p0) REVERT: A 538 ILE cc_start: 0.6177 (pt) cc_final: 0.5894 (pt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.0752 time to fit residues: 15.5349 Evaluate side-chains 112 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN C 752 GLN A 260 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 752 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.167074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145239 restraints weight = 19633.722| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.15 r_work: 0.3973 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10426 Z= 0.181 Angle : 0.628 5.934 14158 Z= 0.337 Chirality : 0.043 0.163 1660 Planarity : 0.004 0.033 1720 Dihedral : 10.831 88.861 1486 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 5.19 % Allowed : 33.15 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.23), residues: 1240 helix: -1.22 (0.19), residues: 650 sheet: -1.52 (0.49), residues: 120 loop : -1.61 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 668 TYR 0.013 0.002 TYR A 113 PHE 0.036 0.002 PHE A 87 TRP 0.006 0.001 TRP C 277 HIS 0.005 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (10426) covalent geometry : angle 0.62836 / 0.34 (14158) hydrogen bonds : bond 0.05883 / 3.79 ( 352) hydrogen bonds : angle 5.41526 / 3.80 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 ASP cc_start: 0.4047 (m-30) cc_final: 0.2447 (p0) REVERT: C 538 ILE cc_start: 0.6707 (pt) cc_final: 0.6441 (pt) REVERT: C 744 ASN cc_start: 0.7655 (m110) cc_final: 0.7406 (m110) REVERT: C 752 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: A 402 ASP cc_start: 0.4013 (m-30) cc_final: 0.2461 (p0) REVERT: A 538 ILE cc_start: 0.6685 (pt) cc_final: 0.6410 (pt) REVERT: A 744 ASN cc_start: 0.7694 (m110) cc_final: 0.7449 (m110) REVERT: A 752 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6747 (tm-30) outliers start: 56 outliers final: 36 residues processed: 167 average time/residue: 0.0710 time to fit residues: 18.2551 Evaluate side-chains 147 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 411 TRP Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 596 GLN Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 749 GLN Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 752 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 39 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 384 GLN ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.168736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.146949 restraints weight = 19626.806| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 3.17 r_work: 0.4002 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10426 Z= 0.124 Angle : 0.550 4.918 14158 Z= 0.296 Chirality : 0.040 0.152 1660 Planarity : 0.004 0.031 1720 Dihedral : 10.693 88.222 1486 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.52 % Allowed : 34.44 % 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 are not related in a simple way. whole: -1.94 (0.23), residues: 1240 helix: -0.96 (0.19), residues: 652 sheet: -1.44 (0.50), residues: 118 loop : -1.50 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 711 TYR 0.008 0.001 TYR C 228 PHE 0.010 0.001 PHE A 287 TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10426) covalent geometry : angle 0.55042 / 0.30 (14158) hydrogen bonds : bond 0.04844 / 3.06 ( 352) hydrogen bonds : angle 5.09345 / 3.56 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 LEU cc_start: 0.6329 (mm) cc_final: 0.6099 (tp) REVERT: C 212 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6934 (ttm) REVERT: C 384 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: C 402 ASP cc_start: 0.3837 (m-30) cc_final: 0.2399 (p0) REVERT: C 680 MET cc_start: 0.7084 (mmt) cc_final: 0.6858 (mmt) REVERT: C 744 ASN cc_start: 0.7528 (m110) cc_final: 0.7275 (m110) REVERT: A 212 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6926 (ttm) REVERT: A 384 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: A 402 ASP cc_start: 0.3802 (m-30) cc_final: 0.2400 (p0) REVERT: A 680 MET cc_start: 0.7096 (mmt) cc_final: 0.6869 (mmt) outliers start: 38 outliers final: 22 residues processed: 152 average time/residue: 0.0646 time to fit residues: 15.0332 Evaluate side-chains 136 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 384 GLN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 411 TRP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A 747 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.166055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.144091 restraints weight = 19861.832| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.19 r_work: 0.3964 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10426 Z= 0.166 Angle : 0.593 6.043 14158 Z= 0.315 Chirality : 0.042 0.145 1660 Planarity : 0.004 0.032 1720 Dihedral : 10.726 89.124 1486 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 6.67 % Allowed : 32.13 % Favored : 61.20 % 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 are not related in a simple way. whole: -2.11 (0.23), residues: 1240 helix: -1.05 (0.19), residues: 664 sheet: -1.54 (0.50), residues: 118 loop : -1.65 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 745 TYR 0.018 0.002 TYR A 474 PHE 0.039 0.002 PHE C 87 TRP 0.010 0.001 TRP C 95 HIS 0.003 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10426) covalent geometry : angle 0.59296 / 0.32 (14158) hydrogen bonds : bond 0.04953 / 3.12 ( 352) hydrogen bonds : angle 5.04535 / 3.54 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 112 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 402 ASP cc_start: 0.4018 (m-30) cc_final: 0.2418 (p0) REVERT: C 538 ILE cc_start: 0.6798 (pt) cc_final: 0.6534 (pt) REVERT: C 744 ASN cc_start: 0.7520 (m110) cc_final: 0.7246 (m110) REVERT: A 212 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7000 (ttm) REVERT: A 402 ASP cc_start: 0.3891 (m-30) cc_final: 0.2397 (p0) REVERT: A 538 ILE cc_start: 0.6797 (pt) cc_final: 0.6526 (pt) outliers start: 72 outliers final: 52 residues processed: 168 average time/residue: 0.0591 time to fit residues: 15.8366 Evaluate side-chains 159 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 411 TRP Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 0.0040 chunk 109 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A 747 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.146373 restraints weight = 19693.762| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.18 r_work: 0.3992 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10426 Z= 0.117 Angle : 0.544 8.177 14158 Z= 0.289 Chirality : 0.040 0.143 1660 Planarity : 0.003 0.030 1720 Dihedral : 10.681 89.071 1486 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 6.20 % Allowed : 32.87 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.23), residues: 1240 helix: -0.83 (0.19), residues: 670 sheet: -1.44 (0.50), residues: 118 loop : -1.49 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 745 TYR 0.014 0.001 TYR A 474 PHE 0.015 0.001 PHE A 287 TRP 0.012 0.001 TRP C 95 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (10426) covalent geometry : angle 0.54363 / 0.29 (14158) hydrogen bonds : bond 0.04261 / 2.66 ( 352) hydrogen bonds : angle 4.79405 / 3.35 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6155 (tp) REVERT: C 402 ASP cc_start: 0.3844 (m-30) cc_final: 0.2370 (p0) REVERT: C 538 ILE cc_start: 0.6620 (pt) cc_final: 0.6354 (pt) REVERT: C 657 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6317 (mmm) REVERT: C 694 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.4084 (mm) REVERT: A 209 LEU cc_start: 0.6379 (mm) cc_final: 0.6136 (tp) REVERT: A 238 CYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 402 ASP cc_start: 0.3758 (m-30) cc_final: 0.2350 (p0) REVERT: A 538 ILE cc_start: 0.6592 (pt) cc_final: 0.6319 (pt) REVERT: A 657 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6295 (mmm) REVERT: A 694 LEU cc_start: 0.4274 (OUTLIER) cc_final: 0.4066 (mm) outliers start: 67 outliers final: 46 residues processed: 167 average time/residue: 0.0652 time to fit residues: 16.5143 Evaluate side-chains 161 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 33 optimal weight: 0.0020 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.167352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.145620 restraints weight = 19867.238| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.17 r_work: 0.3986 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10426 Z= 0.135 Angle : 0.566 8.130 14158 Z= 0.297 Chirality : 0.041 0.150 1660 Planarity : 0.004 0.061 1720 Dihedral : 10.610 89.333 1486 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 6.30 % Allowed : 32.87 % Favored : 60.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.23), residues: 1240 helix: -0.80 (0.19), residues: 674 sheet: -1.37 (0.51), residues: 112 loop : -1.59 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.011 0.001 TYR A 474 PHE 0.017 0.001 PHE A 415 TRP 0.011 0.001 TRP C 95 HIS 0.003 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10426) covalent geometry : angle 0.56580 / 0.30 (14158) hydrogen bonds : bond 0.04343 / 2.70 ( 352) hydrogen bonds : angle 4.73970 / 3.30 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 110 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7535 (m) REVERT: C 402 ASP cc_start: 0.3875 (m-30) cc_final: 0.2410 (p0) REVERT: C 538 ILE cc_start: 0.6730 (pt) cc_final: 0.6455 (pt) REVERT: C 694 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.4086 (mm) REVERT: A 402 ASP cc_start: 0.3801 (m-30) cc_final: 0.2385 (p0) REVERT: A 538 ILE cc_start: 0.6734 (pt) cc_final: 0.6456 (pt) REVERT: A 694 LEU cc_start: 0.4287 (OUTLIER) cc_final: 0.4080 (mm) outliers start: 68 outliers final: 52 residues processed: 166 average time/residue: 0.0629 time to fit residues: 16.3853 Evaluate side-chains 158 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.167348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.145523 restraints weight = 19757.848| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.17 r_work: 0.3982 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10426 Z= 0.129 Angle : 0.568 7.432 14158 Z= 0.298 Chirality : 0.040 0.158 1660 Planarity : 0.004 0.050 1720 Dihedral : 10.574 89.598 1486 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 6.67 % Allowed : 33.24 % Favored : 60.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1240 helix: -0.74 (0.20), residues: 674 sheet: -1.39 (0.52), residues: 112 loop : -1.52 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.010 0.001 TYR C 474 PHE 0.046 0.002 PHE C 87 TRP 0.013 0.001 TRP A 95 HIS 0.003 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10426) covalent geometry : angle 0.56758 / 0.30 (14158) hydrogen bonds : bond 0.04256 / 2.64 ( 352) hydrogen bonds : angle 4.70213 / 3.28 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 113 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7531 (m) REVERT: C 402 ASP cc_start: 0.3871 (m-30) cc_final: 0.2446 (p0) REVERT: C 538 ILE cc_start: 0.6694 (pt) cc_final: 0.6421 (pt) REVERT: C 657 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6292 (mmm) REVERT: C 694 LEU cc_start: 0.4401 (OUTLIER) cc_final: 0.4191 (mm) REVERT: A 242 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.4118 (mpt180) REVERT: A 402 ASP cc_start: 0.3805 (m-30) cc_final: 0.2421 (p0) REVERT: A 538 ILE cc_start: 0.6694 (pt) cc_final: 0.6403 (pt) REVERT: A 657 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6266 (mmm) REVERT: A 694 LEU cc_start: 0.4426 (OUTLIER) cc_final: 0.4210 (mm) outliers start: 72 outliers final: 56 residues processed: 170 average time/residue: 0.0633 time to fit residues: 16.7143 Evaluate side-chains 166 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 104 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.167482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.145691 restraints weight = 19711.166| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.15 r_work: 0.3989 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10426 Z= 0.123 Angle : 0.563 7.385 14158 Z= 0.295 Chirality : 0.040 0.163 1660 Planarity : 0.004 0.044 1720 Dihedral : 10.480 89.696 1486 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 6.76 % Allowed : 33.70 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.24), residues: 1240 helix: -0.69 (0.20), residues: 676 sheet: -1.43 (0.52), residues: 112 loop : -1.51 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 132 TYR 0.010 0.001 TYR A 474 PHE 0.046 0.002 PHE A 87 TRP 0.011 0.001 TRP A 95 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10426) covalent geometry : angle 0.56256 / 0.29 (14158) hydrogen bonds : bond 0.04122 / 2.56 ( 352) hydrogen bonds : angle 4.63885 / 3.22 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 109 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7387 (m) REVERT: C 242 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.4186 (mpt180) REVERT: C 402 ASP cc_start: 0.3903 (m-30) cc_final: 0.2535 (p0) REVERT: C 538 ILE cc_start: 0.6586 (pt) cc_final: 0.6300 (pt) REVERT: C 657 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6272 (mmm) REVERT: C 694 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.4213 (mm) REVERT: A 238 CYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7400 (m) REVERT: A 242 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.4191 (mpt180) REVERT: A 402 ASP cc_start: 0.3821 (m-30) cc_final: 0.2488 (p0) REVERT: A 423 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6206 (mp0) REVERT: A 538 ILE cc_start: 0.6597 (pt) cc_final: 0.6305 (pt) REVERT: A 657 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6268 (mmm) REVERT: A 694 LEU cc_start: 0.4415 (OUTLIER) cc_final: 0.4189 (mm) outliers start: 73 outliers final: 59 residues processed: 167 average time/residue: 0.0621 time to fit residues: 15.8761 Evaluate side-chains 169 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 102 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 0.0170 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.168066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.146250 restraints weight = 19694.061| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.16 r_work: 0.3992 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10426 Z= 0.116 Angle : 0.557 7.398 14158 Z= 0.292 Chirality : 0.040 0.167 1660 Planarity : 0.004 0.040 1720 Dihedral : 10.393 89.706 1486 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 6.20 % Allowed : 34.17 % Favored : 59.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1240 helix: -0.61 (0.20), residues: 676 sheet: -1.43 (0.52), residues: 112 loop : -1.48 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.009 0.001 TYR A 474 PHE 0.049 0.002 PHE A 87 TRP 0.012 0.001 TRP A 95 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (10426) covalent geometry : angle 0.55697 / 0.29 (14158) hydrogen bonds : bond 0.04003 / 2.47 ( 352) hydrogen bonds : angle 4.58187 / 3.18 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 108 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7315 (m) REVERT: C 242 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.4167 (mpt180) REVERT: C 402 ASP cc_start: 0.3891 (m-30) cc_final: 0.2600 (p0) REVERT: C 538 ILE cc_start: 0.6567 (pt) cc_final: 0.6296 (pt) REVERT: C 657 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6266 (mmm) REVERT: C 728 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7696 (mp) REVERT: A 238 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7342 (m) REVERT: A 242 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.4167 (mpt180) REVERT: A 402 ASP cc_start: 0.3790 (m-30) cc_final: 0.2522 (p0) REVERT: A 423 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6208 (mp0) REVERT: A 538 ILE cc_start: 0.6580 (pt) cc_final: 0.6296 (pt) REVERT: A 657 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6267 (mmm) REVERT: A 728 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7699 (mp) outliers start: 67 outliers final: 51 residues processed: 161 average time/residue: 0.0634 time to fit residues: 15.4616 Evaluate side-chains 162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 103 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 91 optimal weight: 0.0040 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0040 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.0070 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.171089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.149299 restraints weight = 19394.252| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.15 r_work: 0.4029 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10426 Z= 0.097 Angle : 0.538 7.642 14158 Z= 0.281 Chirality : 0.039 0.169 1660 Planarity : 0.004 0.031 1720 Dihedral : 10.303 88.980 1486 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.61 % Allowed : 36.67 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.24), residues: 1240 helix: -0.44 (0.20), residues: 680 sheet: -1.47 (0.49), residues: 120 loop : -1.42 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 438 TYR 0.008 0.001 TYR A 474 PHE 0.049 0.001 PHE A 87 TRP 0.013 0.001 TRP A 95 HIS 0.004 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (10426) covalent geometry : angle 0.53793 / 0.28 (14158) hydrogen bonds : bond 0.03492 / 2.13 ( 352) hydrogen bonds : angle 4.38790 / 3.04 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7404 (m) REVERT: C 402 ASP cc_start: 0.3908 (m-30) cc_final: 0.2848 (p0) REVERT: C 423 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6089 (mp0) REVERT: C 657 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6260 (mmm) REVERT: A 259 VAL cc_start: 0.5301 (OUTLIER) cc_final: 0.5056 (t) REVERT: A 402 ASP cc_start: 0.3948 (m-30) cc_final: 0.2878 (p0) REVERT: A 423 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6138 (mp0) REVERT: A 657 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6285 (mmm) outliers start: 39 outliers final: 33 residues processed: 154 average time/residue: 0.0764 time to fit residues: 18.2372 Evaluate side-chains 148 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 670 PHE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 728 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.169157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147380 restraints weight = 19550.368| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.15 r_work: 0.4005 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10426 Z= 0.113 Angle : 0.548 7.301 14158 Z= 0.288 Chirality : 0.040 0.166 1660 Planarity : 0.004 0.035 1720 Dihedral : 10.209 89.458 1486 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.26 % Allowed : 36.02 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.24), residues: 1240 helix: -0.44 (0.20), residues: 682 sheet: -1.49 (0.49), residues: 118 loop : -1.47 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 438 TYR 0.010 0.001 TYR A 228 PHE 0.049 0.001 PHE A 87 TRP 0.010 0.001 TRP A 95 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10426) covalent geometry : angle 0.54755 / 0.29 (14158) hydrogen bonds : bond 0.03759 / 2.33 ( 352) hydrogen bonds : angle 4.46130 / 3.09 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.48 seconds wall clock time: 34 minutes 6.92 seconds (2046.92 seconds total)