Starting phenix.real_space_refine on Sat Mar 7 07:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tqh_10551/03_2026/6tqh_10551_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tqh_10551/03_2026/6tqh_10551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tqh_10551/03_2026/6tqh_10551_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tqh_10551/03_2026/6tqh_10551_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tqh_10551/03_2026/6tqh_10551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tqh_10551/03_2026/6tqh_10551.map" } resolution = 3.4 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= 0.002 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 8 5.49 5 S 92 5.16 5 C 12620 2.51 5 N 3384 2.21 5 O 3778 1.98 5 H 19793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "F" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6486 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "C" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6487 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "B" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' FE': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' FE': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.70, per 1000 atoms: 0.17 Number of scatterers: 39677 At special positions: 0 Unit cell: (120.91, 116.39, 142.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 92 16.00 P 8 15.00 O 3778 8.00 N 3384 7.00 C 12620 6.00 H 19793 1.00 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: 3.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4804 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 14 sheets defined 54.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 removed outlier: 3.510A pdb=" N LEU A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 44 removed outlier: 4.255A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.855A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 81 removed outlier: 4.078A pdb=" N ILE A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.512A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.637A pdb=" N ALA A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 174 through 182 removed outlier: 3.824A pdb=" N SER A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 256 through 269 removed outlier: 4.606A pdb=" N ASP A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.608A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.559A pdb=" N GLU A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.524A pdb=" N ALA A 333 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.675A pdb=" N LYS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.711A pdb=" N GLY A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 removed outlier: 3.550A pdb=" N HIS A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 437' Processing helix chain 'A' and resid 466 through 475 removed outlier: 3.944A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.571A pdb=" N ASN A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 removed outlier: 4.837A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 removed outlier: 3.535A pdb=" N LEU A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.254A pdb=" N LYS A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 560 " --> pdb=" O TRP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 624 through 628 removed outlier: 3.864A pdb=" N THR A 628 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.694A pdb=" N LEU A 638 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 639 " --> pdb=" O ALA A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 639' Processing helix chain 'A' and resid 643 through 663 removed outlier: 3.724A pdb=" N CYS A 647 " --> pdb=" O PRO A 643 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 661 " --> pdb=" O HIS A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.771A pdb=" N ALA A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.631A pdb=" N HIS A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 removed outlier: 4.394A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 753 removed outlier: 3.504A pdb=" N LEU A 743 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 775 through 783 removed outlier: 3.518A pdb=" N ALA A 779 " --> pdb=" O TYR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 808 Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.800A pdb=" N GLY A 819 " --> pdb=" O ARG A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 829 through 838 removed outlier: 3.569A pdb=" N GLU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.610A pdb=" N ALA A 844 " --> pdb=" O CYS A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 855 through 863 removed outlier: 4.226A pdb=" N THR A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 472 Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 495 through 498 removed outlier: 3.531A pdb=" N GLN F 498 " --> pdb=" O TYR F 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 499 through 505 Processing helix chain 'F' and resid 521 through 536 Processing helix chain 'F' and resid 548 through 561 removed outlier: 4.515A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 569 Processing helix chain 'F' and resid 624 through 628 Processing helix chain 'F' and resid 635 through 639 removed outlier: 3.614A pdb=" N LEU F 638 " --> pdb=" O ASP F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 660 removed outlier: 3.859A pdb=" N PHE F 649 " --> pdb=" O SER F 645 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F 655 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 668 through 671 Processing helix chain 'F' and resid 672 through 681 removed outlier: 3.551A pdb=" N LEU F 681 " --> pdb=" O GLN F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 692 Processing helix chain 'F' and resid 693 through 695 No H-bonds generated for 'chain 'F' and resid 693 through 695' Processing helix chain 'F' and resid 696 through 715 removed outlier: 3.980A pdb=" N HIS F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 708 " --> pdb=" O HIS F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 732 Processing helix chain 'F' and resid 736 through 753 removed outlier: 3.604A pdb=" N LEU F 743 " --> pdb=" O LEU F 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS F 746 " --> pdb=" O ALA F 742 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG F 750 " --> pdb=" O CYS F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 783 removed outlier: 4.190A pdb=" N ALA F 776 " --> pdb=" O ARG F 772 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 779 " --> pdb=" O TYR F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 792 through 808 removed outlier: 3.871A pdb=" N GLU F 796 " --> pdb=" O ALA F 792 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 808 " --> pdb=" O THR F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 819 Processing helix chain 'F' and resid 821 through 827 removed outlier: 3.635A pdb=" N ALA F 827 " --> pdb=" O ALA F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 828 through 838 removed outlier: 3.939A pdb=" N PHE F 837 " --> pdb=" O SER F 833 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP F 838 " --> pdb=" O GLU F 834 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 845 removed outlier: 3.607A pdb=" N ASN F 845 " --> pdb=" O THR F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 863 removed outlier: 3.693A pdb=" N LYS F 855 " --> pdb=" O ILE F 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F 857 " --> pdb=" O GLU F 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 487 through 493 Processing helix chain 'C' and resid 495 through 498 removed outlier: 3.531A pdb=" N GLN C 498 " --> pdb=" O TYR C 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 499 through 505 Processing helix chain 'C' and resid 521 through 536 Processing helix chain 'C' and resid 548 through 561 removed outlier: 4.515A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 Processing helix chain 'C' and resid 624 through 628 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.614A pdb=" N LEU C 638 " --> pdb=" O ASP C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 660 removed outlier: 3.859A pdb=" N PHE C 649 " --> pdb=" O SER C 645 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 671 Processing helix chain 'C' and resid 672 through 681 removed outlier: 3.551A pdb=" N LEU C 681 " --> pdb=" O GLN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 692 Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.980A pdb=" N HIS C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 708 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 Processing helix chain 'C' and resid 736 through 753 removed outlier: 3.604A pdb=" N LEU C 743 " --> pdb=" O LEU C 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS C 746 " --> pdb=" O ALA C 742 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 750 " --> pdb=" O CYS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 783 removed outlier: 4.189A pdb=" N ALA C 776 " --> pdb=" O ARG C 772 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 779 " --> pdb=" O TYR C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 808 removed outlier: 3.871A pdb=" N GLU C 796 " --> pdb=" O ALA C 792 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 808 " --> pdb=" O THR C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 821 through 827 removed outlier: 3.634A pdb=" N ALA C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 838 removed outlier: 3.939A pdb=" N PHE C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 845 removed outlier: 3.607A pdb=" N ASN C 845 " --> pdb=" O THR C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 863 removed outlier: 3.693A pdb=" N LYS C 855 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.511A pdb=" N LEU B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.254A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.855A pdb=" N LEU B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 81 removed outlier: 4.079A pdb=" N ILE B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.511A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 142 through 158 removed outlier: 3.638A pdb=" N ALA B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.823A pdb=" N SER B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 256 through 269 removed outlier: 4.607A pdb=" N ASP B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.609A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.559A pdb=" N GLU B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.525A pdb=" N ALA B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.676A pdb=" N LYS B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.711A pdb=" N GLY B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 removed outlier: 3.550A pdb=" N HIS B 437 " --> pdb=" O GLY B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 437' Processing helix chain 'B' and resid 466 through 475 removed outlier: 3.945A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.572A pdb=" N ASN B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 4.837A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 removed outlier: 3.535A pdb=" N LEU B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.253A pdb=" N LYS B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 560 " --> pdb=" O TRP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.864A pdb=" N THR B 628 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.694A pdb=" N LEU B 638 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 639 " --> pdb=" O ALA B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 635 through 639' Processing helix chain 'B' and resid 643 through 663 removed outlier: 3.724A pdb=" N CYS B 647 " --> pdb=" O PRO B 643 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 661 " --> pdb=" O HIS B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 680 removed outlier: 3.772A pdb=" N ALA B 675 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 696 through 715 removed outlier: 3.631A pdb=" N HIS B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 730 removed outlier: 4.395A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 753 removed outlier: 3.503A pdb=" N LEU B 743 " --> pdb=" O LEU B 739 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 744 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 775 through 783 removed outlier: 3.519A pdb=" N ALA B 779 " --> pdb=" O TYR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 808 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.801A pdb=" N GLY B 819 " --> pdb=" O ARG B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 829 through 838 removed outlier: 3.568A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.611A pdb=" N ALA B 844 " --> pdb=" O CYS B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 855 through 863 removed outlier: 4.227A pdb=" N THR B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.797A pdb=" N SER A 90 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 98 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER B 369 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR B 372 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 220 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 219 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL B 255 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 221 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 272 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 322 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 5.999A pdb=" N CYS A 108 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.871A pdb=" N TYR A 272 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 322 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 319 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET A 343 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY A 321 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ARG A 345 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 219 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL A 255 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 221 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR A 372 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 220 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 369 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 394 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 98 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 90 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 462 removed outlier: 6.270A pdb=" N TYR A 461 " --> pdb=" O VAL A 634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.635A pdb=" N ILE A 484 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLU A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR A 486 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 460 through 461 removed outlier: 6.933A pdb=" N MET F 592 " --> pdb=" O MET F 631 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE F 633 " --> pdb=" O MET F 592 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA F 594 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE F 540 " --> pdb=" O ILE F 593 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL F 595 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA F 542 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG F 481 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE F 541 " --> pdb=" O ARG F 481 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 483 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA F 482 " --> pdb=" O GLU F 511 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE F 513 " --> pdb=" O ALA F 482 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE F 484 " --> pdb=" O PHE F 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 460 through 461 removed outlier: 6.934A pdb=" N MET C 592 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE C 633 " --> pdb=" O MET C 592 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA C 594 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE C 540 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL C 595 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA C 542 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG C 481 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 541 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 483 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 482 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE C 513 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE C 484 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'B' and resid 167 through 169 removed outlier: 5.999A pdb=" N CYS B 108 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AB4, first strand: chain 'B' and resid 461 through 462 removed outlier: 6.270A pdb=" N TYR B 461 " --> pdb=" O VAL B 634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 512 through 516 removed outlier: 6.636A pdb=" N ILE B 484 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLU B 515 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR B 486 " --> pdb=" O GLU B 515 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.09 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19767 1.02 - 1.21: 30 1.21 - 1.41: 8227 1.41 - 1.61: 11899 1.61 - 1.81: 166 Bond restraints: 40089 Sorted by residual: bond pdb=" C ARG B 865 " pdb=" N ASP B 866 " ideal model delta sigma weight residual 1.331 1.554 -0.223 1.38e-02 5.25e+03 2.60e+02 bond pdb=" C ARG A 865 " pdb=" N ASP A 866 " ideal model delta sigma weight residual 1.331 1.553 -0.222 1.38e-02 5.25e+03 2.59e+02 bond pdb=" O5D NAD B 901 " pdb=" PN NAD B 901 " ideal model delta sigma weight residual 1.637 1.777 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O5D NAD A 902 " pdb=" PN NAD A 902 " ideal model delta sigma weight residual 1.637 1.776 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O5D NAD A 901 " pdb=" PN NAD A 901 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 40084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.15: 72574 7.15 - 14.30: 46 14.30 - 21.46: 6 21.46 - 28.61: 8 28.61 - 35.76: 14 Bond angle restraints: 72648 Sorted by residual: angle pdb=" CG2 THR B 27 " pdb=" CB THR B 27 " pdb=" HB THR B 27 " ideal model delta sigma weight residual 108.00 72.24 35.76 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CG2 THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 108.00 73.55 34.45 3.00e+00 1.11e-01 1.32e+02 angle pdb=" OG1 THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 109.00 75.81 33.19 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA THR B 27 " pdb=" CB THR B 27 " pdb=" HB THR B 27 " ideal model delta sigma weight residual 109.00 77.12 31.88 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CA THR B 616 " pdb=" CB THR B 616 " pdb=" HB THR B 616 " ideal model delta sigma weight residual 109.00 77.61 31.39 3.00e+00 1.11e-01 1.10e+02 ... (remaining 72643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16926 17.98 - 35.96: 1593 35.96 - 53.94: 351 53.94 - 71.92: 122 71.92 - 89.90: 19 Dihedral angle restraints: 19011 sinusoidal: 10416 harmonic: 8595 Sorted by residual: dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N LEU A 417 " pdb=" CA LEU A 417 " ideal model delta harmonic sigma weight residual 180.00 147.04 32.96 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA SER B 416 " pdb=" C SER B 416 " pdb=" N LEU B 417 " pdb=" CA LEU B 417 " ideal model delta harmonic sigma weight residual 180.00 147.10 32.90 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ILE A 405 " pdb=" C ILE A 405 " pdb=" N GLY A 406 " pdb=" CA GLY A 406 " ideal model delta harmonic sigma weight residual 180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 19008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3023 0.109 - 0.217: 109 0.217 - 0.326: 10 0.326 - 0.435: 0 0.435 - 0.544: 4 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CB THR A 27 " pdb=" CA THR A 27 " pdb=" OG1 THR A 27 " pdb=" CG2 THR A 27 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CB THR B 27 " pdb=" CA THR B 27 " pdb=" OG1 THR B 27 " pdb=" CG2 THR B 27 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CB THR B 616 " pdb=" CA THR B 616 " pdb=" OG1 THR B 616 " pdb=" CG2 THR B 616 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.32e+00 ... (remaining 3143 not shown) Planarity restraints: 5992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 628 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 629 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 629 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 629 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 628 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 629 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.038 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 112 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.031 5.00e-02 4.00e+02 ... (remaining 5989 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 188 1.83 - 2.52: 37450 2.52 - 3.21: 125212 3.21 - 3.91: 163759 3.91 - 4.60: 272005 Nonbonded interactions: 598614 Sorted by model distance: nonbonded pdb=" HE1 HIS A 737 " pdb="FE FE A 903 " model vdw 1.137 1.790 nonbonded pdb=" HE1 HIS B 737 " pdb="FE FE B 903 " model vdw 1.140 1.790 nonbonded pdb="HH12 ARG A 579 " pdb=" O TYR A 581 " model vdw 1.465 2.450 nonbonded pdb="HH12 ARG B 579 " pdb=" O TYR B 581 " model vdw 1.466 2.450 nonbonded pdb=" O GLU A 63 " pdb=" HH TYR B 848 " model vdw 1.509 2.450 ... (remaining 598609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 71 through 903)) selection = (chain 'B' and (resid 1 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name HA2 or name HA3)) or resid 435 through 903)) } ncs_group { reference = (chain 'C' and (resid 451 through 715 or (resid 716 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name \ HB2 or name HB3 or name HD21 or name HD22)) or resid 717 through 869)) selection = chain 'F' } 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: 1.100 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: 0.230 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.400 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.013 0.223 20296 Z= 0.544 Angle : 0.924 15.110 27558 Z= 0.455 Chirality : 0.057 0.544 3146 Planarity : 0.005 0.065 3542 Dihedral : 14.919 89.897 7580 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.45 % Allowed : 3.38 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -6.51 (0.11), residues: 2568 helix: -4.81 (0.06), residues: 1254 sheet: -3.96 (0.21), residues: 332 loop : -3.39 (0.16), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 463 TYR 0.013 0.001 TYR C 867 PHE 0.017 0.002 PHE C 763 TRP 0.014 0.002 TRP B 424 HIS 0.006 0.001 HIS F 704 Details of bonding type rmsd covalent geometry : bond 0.01281 (20296) covalent geometry : angle 0.92362 (27558) hydrogen bonds : bond 0.27997 ( 726) hydrogen bonds : angle 11.30960 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8306 (ttm) cc_final: 0.7993 (ttm) REVERT: F 565 HIS cc_start: 0.7411 (m-70) cc_final: 0.6721 (m-70) REVERT: F 820 VAL cc_start: 0.7003 (t) cc_final: 0.6422 (t) REVERT: B 472 ASP cc_start: 0.7613 (t70) cc_final: 0.7340 (t0) REVERT: B 550 ASP cc_start: 0.8218 (m-30) cc_final: 0.7960 (m-30) outliers start: 30 outliers final: 10 residues processed: 344 average time/residue: 0.4072 time to fit residues: 205.0791 Evaluate side-chains 181 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 868 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 677 GLN ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073948 restraints weight = 146360.043| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.98 r_work: 0.3041 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20296 Z= 0.134 Angle : 0.623 10.916 27558 Z= 0.325 Chirality : 0.055 1.412 3146 Planarity : 0.005 0.061 3542 Dihedral : 9.571 89.273 2994 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.11 % Allowed : 8.74 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.14), residues: 2568 helix: -3.14 (0.10), residues: 1272 sheet: -3.60 (0.23), residues: 330 loop : -2.44 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 773 TYR 0.011 0.001 TYR A 848 PHE 0.024 0.001 PHE C 714 TRP 0.013 0.001 TRP B 453 HIS 0.006 0.001 HIS F 561 Details of bonding type rmsd covalent geometry : bond 0.00291 (20296) covalent geometry : angle 0.62303 (27558) hydrogen bonds : bond 0.04282 ( 726) hydrogen bonds : angle 5.52833 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8747 (ttm) cc_final: 0.8274 (ttm) REVERT: A 767 ASP cc_start: 0.8104 (m-30) cc_final: 0.7831 (m-30) REVERT: F 538 ASP cc_start: 0.8341 (m-30) cc_final: 0.8050 (t70) REVERT: F 565 HIS cc_start: 0.7767 (m-70) cc_final: 0.7203 (m-70) REVERT: F 568 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8367 (mt-10) REVERT: F 585 LYS cc_start: 0.8964 (tppt) cc_final: 0.8439 (tptp) REVERT: F 741 ASN cc_start: 0.6246 (m110) cc_final: 0.5924 (m110) REVERT: F 848 TYR cc_start: 0.7580 (t80) cc_final: 0.7186 (t80) REVERT: C 538 ASP cc_start: 0.8784 (t0) cc_final: 0.8515 (t0) REVERT: C 558 MET cc_start: 0.8964 (mmm) cc_final: 0.8733 (mmm) REVERT: C 581 TYR cc_start: 0.8135 (t80) cc_final: 0.7855 (t80) REVERT: B 431 GLU cc_start: 0.8157 (tt0) cc_final: 0.7927 (tt0) REVERT: B 443 THR cc_start: 0.9273 (m) cc_final: 0.8970 (p) REVERT: B 449 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 472 ASP cc_start: 0.8329 (t70) cc_final: 0.7928 (t0) REVERT: B 593 ILE cc_start: 0.9008 (tt) cc_final: 0.8768 (tt) outliers start: 23 outliers final: 15 residues processed: 230 average time/residue: 0.3563 time to fit residues: 126.4343 Evaluate side-chains 188 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain F residue 640 MET Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 157 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 410 ASN A 479 HIS A 716 ASN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 479 HIS B 716 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.059832 restraints weight = 154050.121| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.82 r_work: 0.2751 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 20296 Z= 0.277 Angle : 0.673 11.027 27558 Z= 0.353 Chirality : 0.056 1.397 3146 Planarity : 0.005 0.084 3542 Dihedral : 8.503 87.491 2988 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.01 % Allowed : 11.26 % Favored : 87.73 % 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: -3.44 (0.15), residues: 2568 helix: -2.03 (0.12), residues: 1310 sheet: -3.41 (0.24), residues: 330 loop : -1.84 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 577 TYR 0.013 0.001 TYR F 581 PHE 0.021 0.001 PHE A 714 TRP 0.014 0.002 TRP C 453 HIS 0.007 0.002 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00629 (20296) covalent geometry : angle 0.67308 (27558) hydrogen bonds : bond 0.03883 ( 726) hydrogen bonds : angle 4.68276 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8926 (ttm) cc_final: 0.8537 (ttm) REVERT: A 538 ASP cc_start: 0.8814 (m-30) cc_final: 0.8229 (t0) REVERT: A 767 ASP cc_start: 0.8447 (m-30) cc_final: 0.8096 (m-30) REVERT: F 458 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8309 (pttp) REVERT: F 538 ASP cc_start: 0.8838 (m-30) cc_final: 0.8504 (t0) REVERT: F 565 HIS cc_start: 0.7994 (m-70) cc_final: 0.7714 (m-70) REVERT: F 586 MET cc_start: 0.8360 (ptp) cc_final: 0.8148 (ptp) REVERT: F 630 ASP cc_start: 0.8550 (m-30) cc_final: 0.8115 (t0) REVERT: F 646 LEU cc_start: 0.8577 (tp) cc_final: 0.8366 (tp) REVERT: F 659 MET cc_start: 0.8886 (mtt) cc_final: 0.8590 (mtt) REVERT: F 672 ASP cc_start: 0.7944 (m-30) cc_final: 0.7683 (m-30) REVERT: F 848 TYR cc_start: 0.8415 (t80) cc_final: 0.7740 (t80) REVERT: F 858 LEU cc_start: 0.9122 (mm) cc_final: 0.8841 (mm) REVERT: C 538 ASP cc_start: 0.8815 (t0) cc_final: 0.8544 (t0) REVERT: C 592 MET cc_start: 0.9047 (tmm) cc_final: 0.8613 (tpp) REVERT: C 852 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.8834 (t) REVERT: B 249 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 407 ASP cc_start: 0.7754 (t70) cc_final: 0.7322 (t70) REVERT: B 443 THR cc_start: 0.9413 (m) cc_final: 0.9071 (p) REVERT: B 472 ASP cc_start: 0.8406 (t70) cc_final: 0.8074 (t0) outliers start: 21 outliers final: 14 residues processed: 187 average time/residue: 0.3523 time to fit residues: 102.4488 Evaluate side-chains 159 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 593 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 60 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 737 HIS ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.061289 restraints weight = 151292.821| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.86 r_work: 0.2773 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20296 Z= 0.135 Angle : 0.549 11.036 27558 Z= 0.284 Chirality : 0.054 1.410 3146 Planarity : 0.004 0.057 3542 Dihedral : 7.919 88.987 2983 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.82 % Allowed : 12.51 % Favored : 86.67 % 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: -2.69 (0.16), residues: 2568 helix: -1.28 (0.13), residues: 1302 sheet: -3.35 (0.24), residues: 334 loop : -1.60 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 21 TYR 0.012 0.001 TYR F 867 PHE 0.019 0.001 PHE B 714 TRP 0.009 0.001 TRP B 453 HIS 0.008 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00300 (20296) covalent geometry : angle 0.54853 (27558) hydrogen bonds : bond 0.02945 ( 726) hydrogen bonds : angle 4.20717 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8865 (ttm) cc_final: 0.8441 (ttm) REVERT: A 538 ASP cc_start: 0.8803 (m-30) cc_final: 0.8323 (t0) REVERT: A 767 ASP cc_start: 0.8352 (m-30) cc_final: 0.7949 (m-30) REVERT: F 458 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8328 (pttp) REVERT: F 538 ASP cc_start: 0.8824 (m-30) cc_final: 0.8448 (t0) REVERT: F 565 HIS cc_start: 0.8058 (m-70) cc_final: 0.7523 (m-70) REVERT: F 568 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8567 (mt-10) REVERT: F 630 ASP cc_start: 0.8543 (m-30) cc_final: 0.8322 (t0) REVERT: F 659 MET cc_start: 0.8806 (mtt) cc_final: 0.8537 (mtt) REVERT: F 672 ASP cc_start: 0.7974 (m-30) cc_final: 0.7744 (m-30) REVERT: F 848 TYR cc_start: 0.8388 (t80) cc_final: 0.7871 (t80) REVERT: F 858 LEU cc_start: 0.9078 (mm) cc_final: 0.8794 (mm) REVERT: C 538 ASP cc_start: 0.8792 (t0) cc_final: 0.8515 (t0) REVERT: C 558 MET cc_start: 0.9123 (mmm) cc_final: 0.8906 (mmm) REVERT: B 389 MET cc_start: 0.9182 (mmm) cc_final: 0.8792 (mmm) REVERT: B 407 ASP cc_start: 0.7715 (t70) cc_final: 0.7442 (t70) REVERT: B 443 THR cc_start: 0.9358 (m) cc_final: 0.9089 (p) REVERT: B 472 ASP cc_start: 0.8474 (t70) cc_final: 0.8150 (t0) REVERT: B 672 ASP cc_start: 0.8222 (m-30) cc_final: 0.7969 (m-30) outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.3011 time to fit residues: 82.2158 Evaluate side-chains 155 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 58 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 229 optimal weight: 0.0870 chunk 233 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 618 GLN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.069893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.060428 restraints weight = 152718.610| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.95 r_work: 0.2754 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20296 Z= 0.111 Angle : 0.522 11.091 27558 Z= 0.268 Chirality : 0.053 1.418 3146 Planarity : 0.004 0.054 3542 Dihedral : 7.589 89.708 2983 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.97 % Allowed : 13.19 % Favored : 85.85 % 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: -2.08 (0.17), residues: 2568 helix: -0.70 (0.14), residues: 1304 sheet: -3.39 (0.24), residues: 322 loop : -1.33 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.009 0.001 TYR A 848 PHE 0.019 0.001 PHE B 714 TRP 0.008 0.001 TRP B 453 HIS 0.005 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00251 (20296) covalent geometry : angle 0.52164 (27558) hydrogen bonds : bond 0.02715 ( 726) hydrogen bonds : angle 3.96814 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8889 (ttm) cc_final: 0.8487 (ttm) REVERT: A 538 ASP cc_start: 0.8814 (m-30) cc_final: 0.8364 (t0) REVERT: A 767 ASP cc_start: 0.8343 (m-30) cc_final: 0.7928 (m-30) REVERT: F 538 ASP cc_start: 0.8825 (m-30) cc_final: 0.8491 (t0) REVERT: F 565 HIS cc_start: 0.8151 (m-70) cc_final: 0.7402 (m-70) REVERT: F 568 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8599 (mt-10) REVERT: F 586 MET cc_start: 0.8480 (ptp) cc_final: 0.7936 (ptp) REVERT: F 646 LEU cc_start: 0.8602 (tp) cc_final: 0.8357 (tp) REVERT: F 672 ASP cc_start: 0.7892 (m-30) cc_final: 0.7642 (m-30) REVERT: F 848 TYR cc_start: 0.8386 (t80) cc_final: 0.7827 (t80) REVERT: C 538 ASP cc_start: 0.8818 (t0) cc_final: 0.8475 (t0) REVERT: C 558 MET cc_start: 0.9022 (mmm) cc_final: 0.8785 (mmm) REVERT: C 582 LYS cc_start: 0.9452 (ttmm) cc_final: 0.9001 (mttt) REVERT: C 624 ASP cc_start: 0.8985 (t0) cc_final: 0.8592 (t0) REVERT: C 852 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.9040 (t) REVERT: B 389 MET cc_start: 0.9206 (mmm) cc_final: 0.8864 (mmm) REVERT: B 407 ASP cc_start: 0.7786 (t70) cc_final: 0.7514 (t70) REVERT: B 443 THR cc_start: 0.9312 (m) cc_final: 0.9096 (p) REVERT: B 472 ASP cc_start: 0.8478 (t70) cc_final: 0.8208 (t0) REVERT: B 586 MET cc_start: 0.8439 (ptm) cc_final: 0.7987 (ptm) REVERT: B 631 MET cc_start: 0.9065 (tmm) cc_final: 0.8849 (tmm) REVERT: B 672 ASP cc_start: 0.8177 (m-30) cc_final: 0.7876 (m-30) outliers start: 20 outliers final: 13 residues processed: 172 average time/residue: 0.2970 time to fit residues: 82.9934 Evaluate side-chains 160 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 21 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 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 = 0.3013 r_free = 0.3013 target = 0.066871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.057524 restraints weight = 154793.299| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.88 r_work: 0.2687 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20296 Z= 0.194 Angle : 0.566 11.058 27558 Z= 0.295 Chirality : 0.054 1.413 3146 Planarity : 0.004 0.053 3542 Dihedral : 7.526 88.820 2982 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.26 % Allowed : 13.24 % Favored : 85.51 % 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: -1.72 (0.17), residues: 2568 helix: -0.38 (0.14), residues: 1300 sheet: -3.27 (0.24), residues: 342 loop : -1.11 (0.23), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 447 TYR 0.011 0.001 TYR B 848 PHE 0.017 0.001 PHE B 714 TRP 0.011 0.001 TRP F 453 HIS 0.008 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00428 (20296) covalent geometry : angle 0.56632 (27558) hydrogen bonds : bond 0.02910 ( 726) hydrogen bonds : angle 4.06572 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8945 (ttm) cc_final: 0.8573 (ttm) REVERT: A 538 ASP cc_start: 0.8868 (m-30) cc_final: 0.8415 (t0) REVERT: F 458 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8470 (pttp) REVERT: F 538 ASP cc_start: 0.8829 (m-30) cc_final: 0.8600 (t0) REVERT: F 565 HIS cc_start: 0.8269 (m-70) cc_final: 0.7846 (m-70) REVERT: F 672 ASP cc_start: 0.8149 (m-30) cc_final: 0.7932 (m-30) REVERT: C 538 ASP cc_start: 0.8841 (t0) cc_final: 0.8609 (t0) REVERT: C 558 MET cc_start: 0.9108 (mmm) cc_final: 0.8850 (mmm) REVERT: C 582 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9064 (mttt) REVERT: C 852 SER cc_start: 0.9461 (OUTLIER) cc_final: 0.9244 (t) REVERT: B 343 MET cc_start: 0.9153 (ttp) cc_final: 0.8914 (ttp) REVERT: B 389 MET cc_start: 0.9218 (mmm) cc_final: 0.8935 (mmm) REVERT: B 407 ASP cc_start: 0.7886 (t70) cc_final: 0.7623 (t70) REVERT: B 443 THR cc_start: 0.9393 (m) cc_final: 0.9125 (p) REVERT: B 472 ASP cc_start: 0.8554 (t70) cc_final: 0.8256 (t0) REVERT: B 538 ASP cc_start: 0.8582 (m-30) cc_final: 0.8203 (t0) REVERT: B 586 MET cc_start: 0.8611 (ptm) cc_final: 0.8180 (ptm) REVERT: B 631 MET cc_start: 0.9188 (tmm) cc_final: 0.8984 (tmm) REVERT: B 660 GLU cc_start: 0.8463 (pt0) cc_final: 0.8194 (pt0) REVERT: B 785 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7970 (p) outliers start: 26 outliers final: 20 residues processed: 162 average time/residue: 0.3464 time to fit residues: 88.5918 Evaluate side-chains 154 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 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 = 0.3001 r_free = 0.3001 target = 0.066349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.057042 restraints weight = 153925.294| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.86 r_work: 0.2676 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20296 Z= 0.185 Angle : 0.551 11.048 27558 Z= 0.286 Chirality : 0.054 1.424 3146 Planarity : 0.004 0.076 3542 Dihedral : 7.320 88.126 2982 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.45 % Allowed : 13.86 % Favored : 84.69 % 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 (0.17), residues: 2568 helix: -0.15 (0.15), residues: 1308 sheet: -3.21 (0.25), residues: 342 loop : -0.96 (0.23), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 488 TYR 0.011 0.001 TYR F 867 PHE 0.018 0.001 PHE B 714 TRP 0.007 0.001 TRP B 453 HIS 0.007 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00408 (20296) covalent geometry : angle 0.55146 (27558) hydrogen bonds : bond 0.02800 ( 726) hydrogen bonds : angle 4.02957 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8933 (ttm) cc_final: 0.8614 (ttm) REVERT: A 538 ASP cc_start: 0.8835 (m-30) cc_final: 0.8323 (t0) REVERT: A 659 MET cc_start: 0.8723 (tpp) cc_final: 0.8350 (mtp) REVERT: F 458 LYS cc_start: 0.8816 (ptmt) cc_final: 0.8490 (pttp) REVERT: F 565 HIS cc_start: 0.8584 (m-70) cc_final: 0.8280 (m-70) REVERT: F 672 ASP cc_start: 0.8142 (m-30) cc_final: 0.7925 (m-30) REVERT: C 517 GLU cc_start: 0.8364 (pm20) cc_final: 0.7970 (mp0) REVERT: C 538 ASP cc_start: 0.8817 (t0) cc_final: 0.8579 (t0) REVERT: C 582 LYS cc_start: 0.9452 (ttmm) cc_final: 0.9081 (mttt) REVERT: B 389 MET cc_start: 0.9236 (mmm) cc_final: 0.8987 (mmm) REVERT: B 443 THR cc_start: 0.9409 (m) cc_final: 0.9120 (p) REVERT: B 472 ASP cc_start: 0.8613 (t70) cc_final: 0.8328 (t0) REVERT: B 538 ASP cc_start: 0.8538 (m-30) cc_final: 0.8159 (t0) REVERT: B 586 MET cc_start: 0.8642 (ptm) cc_final: 0.8215 (ptm) REVERT: B 631 MET cc_start: 0.9169 (tmm) cc_final: 0.8957 (tmm) REVERT: B 785 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7999 (p) outliers start: 30 outliers final: 22 residues processed: 157 average time/residue: 0.3558 time to fit residues: 86.8693 Evaluate side-chains 150 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 104 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 216 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 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 = 0.3036 r_free = 0.3036 target = 0.067873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058550 restraints weight = 152593.073| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.89 r_work: 0.2711 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20296 Z= 0.107 Angle : 0.514 11.125 27558 Z= 0.264 Chirality : 0.054 1.427 3146 Planarity : 0.004 0.049 3542 Dihedral : 7.162 87.064 2982 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.01 % Allowed : 14.25 % Favored : 84.73 % 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: -1.13 (0.18), residues: 2568 helix: 0.13 (0.15), residues: 1306 sheet: -3.13 (0.25), residues: 336 loop : -0.84 (0.23), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.009 0.001 TYR A 848 PHE 0.018 0.001 PHE B 714 TRP 0.007 0.001 TRP B 453 HIS 0.006 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00243 (20296) covalent geometry : angle 0.51406 (27558) hydrogen bonds : bond 0.02562 ( 726) hydrogen bonds : angle 3.84530 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8943 (ttm) cc_final: 0.8594 (ttm) REVERT: A 538 ASP cc_start: 0.8833 (m-30) cc_final: 0.8382 (t0) REVERT: A 659 MET cc_start: 0.8711 (tpp) cc_final: 0.8394 (mtp) REVERT: F 458 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8430 (pttp) REVERT: F 565 HIS cc_start: 0.8533 (m-70) cc_final: 0.8233 (m-70) REVERT: F 672 ASP cc_start: 0.8092 (m-30) cc_final: 0.7849 (m-30) REVERT: C 517 GLU cc_start: 0.8253 (pm20) cc_final: 0.7918 (mp0) REVERT: C 538 ASP cc_start: 0.8814 (t0) cc_final: 0.8576 (t0) REVERT: C 558 MET cc_start: 0.9059 (mmm) cc_final: 0.8802 (mmm) REVERT: C 582 LYS cc_start: 0.9435 (ttmm) cc_final: 0.9108 (mttt) REVERT: B 389 MET cc_start: 0.9198 (mmm) cc_final: 0.8962 (mmm) REVERT: B 443 THR cc_start: 0.9417 (m) cc_final: 0.9188 (p) REVERT: B 472 ASP cc_start: 0.8539 (t70) cc_final: 0.8275 (t0) REVERT: B 538 ASP cc_start: 0.8566 (m-30) cc_final: 0.8208 (t0) REVERT: B 586 MET cc_start: 0.8477 (ptm) cc_final: 0.8232 (ptm) REVERT: B 672 ASP cc_start: 0.8234 (m-30) cc_final: 0.7968 (m-30) REVERT: B 785 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7927 (p) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 0.3454 time to fit residues: 88.4792 Evaluate side-chains 151 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 230 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 238 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 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 = 0.3011 r_free = 0.3011 target = 0.066621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057309 restraints weight = 154286.080| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.88 r_work: 0.2684 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20296 Z= 0.159 Angle : 0.536 11.118 27558 Z= 0.277 Chirality : 0.054 1.424 3146 Planarity : 0.004 0.047 3542 Dihedral : 7.162 84.319 2982 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.11 % Allowed : 14.49 % Favored : 84.40 % 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: -1.05 (0.18), residues: 2568 helix: 0.23 (0.15), residues: 1312 sheet: -3.16 (0.24), residues: 372 loop : -0.70 (0.24), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.009 0.001 TYR F 867 PHE 0.016 0.001 PHE B 714 TRP 0.007 0.001 TRP B 453 HIS 0.007 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00356 (20296) covalent geometry : angle 0.53608 (27558) hydrogen bonds : bond 0.02635 ( 726) hydrogen bonds : angle 3.89460 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8958 (ttm) cc_final: 0.8629 (ttm) REVERT: A 515 GLU cc_start: 0.8331 (mp0) cc_final: 0.8115 (mp0) REVERT: A 538 ASP cc_start: 0.8842 (m-30) cc_final: 0.8394 (t0) REVERT: A 659 MET cc_start: 0.8773 (tpp) cc_final: 0.8454 (mtp) REVERT: F 458 LYS cc_start: 0.8771 (ptmt) cc_final: 0.8450 (pttp) REVERT: F 565 HIS cc_start: 0.8484 (m-70) cc_final: 0.8170 (m-70) REVERT: F 672 ASP cc_start: 0.8178 (m-30) cc_final: 0.7948 (m-30) REVERT: C 517 GLU cc_start: 0.8271 (pm20) cc_final: 0.7899 (mp0) REVERT: C 538 ASP cc_start: 0.8806 (t0) cc_final: 0.8549 (t0) REVERT: C 582 LYS cc_start: 0.9437 (ttmm) cc_final: 0.9104 (mttt) REVERT: C 592 MET cc_start: 0.9121 (tmm) cc_final: 0.8628 (tpp) REVERT: B 389 MET cc_start: 0.9228 (mmm) cc_final: 0.9009 (mmm) REVERT: B 443 THR cc_start: 0.9433 (m) cc_final: 0.9200 (p) REVERT: B 472 ASP cc_start: 0.8571 (t70) cc_final: 0.8319 (t0) REVERT: B 538 ASP cc_start: 0.8547 (m-30) cc_final: 0.8340 (t0) REVERT: B 672 ASP cc_start: 0.8295 (m-30) cc_final: 0.8055 (m-30) REVERT: B 785 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7938 (p) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.3400 time to fit residues: 82.5975 Evaluate side-chains 151 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 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 = 0.3046 r_free = 0.3046 target = 0.068253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058934 restraints weight = 152577.583| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.90 r_work: 0.2711 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20296 Z= 0.095 Angle : 0.506 11.124 27558 Z= 0.259 Chirality : 0.053 1.429 3146 Planarity : 0.003 0.046 3542 Dihedral : 7.002 84.492 2982 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.92 % Allowed : 14.69 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.18), residues: 2568 helix: 0.38 (0.15), residues: 1318 sheet: -3.10 (0.25), residues: 336 loop : -0.74 (0.23), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.008 0.001 TYR F 867 PHE 0.017 0.001 PHE B 714 TRP 0.007 0.001 TRP B 453 HIS 0.006 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00221 (20296) covalent geometry : angle 0.50616 (27558) hydrogen bonds : bond 0.02437 ( 726) hydrogen bonds : angle 3.73628 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8950 (ttm) cc_final: 0.8592 (ttm) REVERT: A 515 GLU cc_start: 0.8318 (mp0) cc_final: 0.8087 (mp0) REVERT: A 538 ASP cc_start: 0.8843 (m-30) cc_final: 0.8356 (t0) REVERT: A 659 MET cc_start: 0.8705 (tpp) cc_final: 0.8466 (mtp) REVERT: F 565 HIS cc_start: 0.8499 (m-70) cc_final: 0.8198 (m-70) REVERT: F 672 ASP cc_start: 0.8075 (m-30) cc_final: 0.7833 (m-30) REVERT: C 517 GLU cc_start: 0.8226 (pm20) cc_final: 0.7793 (mp0) REVERT: C 538 ASP cc_start: 0.8801 (t0) cc_final: 0.8554 (t0) REVERT: C 582 LYS cc_start: 0.9430 (ttmm) cc_final: 0.9058 (mttt) REVERT: C 630 ASP cc_start: 0.9023 (m-30) cc_final: 0.8455 (m-30) REVERT: B 389 MET cc_start: 0.9192 (mmm) cc_final: 0.8968 (mmm) REVERT: B 443 THR cc_start: 0.9396 (m) cc_final: 0.9181 (p) REVERT: B 472 ASP cc_start: 0.8521 (t70) cc_final: 0.8278 (t0) REVERT: B 538 ASP cc_start: 0.8573 (m-30) cc_final: 0.8199 (t0) REVERT: B 672 ASP cc_start: 0.8210 (m-30) cc_final: 0.7976 (m-30) REVERT: B 785 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7899 (p) outliers start: 19 outliers final: 17 residues processed: 154 average time/residue: 0.3353 time to fit residues: 82.0647 Evaluate side-chains 152 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 723 HIS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 785 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 146 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 187 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 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 = 0.3050 r_free = 0.3050 target = 0.068383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.059027 restraints weight = 153325.464| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.92 r_work: 0.2715 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20296 Z= 0.099 Angle : 0.505 11.151 27558 Z= 0.258 Chirality : 0.053 1.426 3146 Planarity : 0.003 0.043 3542 Dihedral : 6.895 82.837 2982 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.97 % Allowed : 14.73 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2568 helix: 0.56 (0.15), residues: 1302 sheet: -3.13 (0.25), residues: 344 loop : -0.68 (0.23), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.007 0.001 TYR F 867 PHE 0.016 0.001 PHE B 714 TRP 0.007 0.001 TRP B 453 HIS 0.006 0.001 HIS C 723 Details of bonding type rmsd covalent geometry : bond 0.00228 (20296) covalent geometry : angle 0.50524 (27558) hydrogen bonds : bond 0.02397 ( 726) hydrogen bonds : angle 3.69384 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.85 seconds wall clock time: 108 minutes 34.49 seconds (6514.49 seconds total)