Starting phenix.real_space_refine on Mon Sep 14 04:57:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.map" model { file = "/net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o6r_0636/09_2026/6o6r_0636.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Na 8 4.78 5 C 18248 2.51 5 N 4484 2.21 5 O 4864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27744 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6812 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 20, 'TRANS': 812} Chain breaks: 9 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 124 Unusual residues: {' NA': 2, '9PE': 1, 'LQ7': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 8.71, per 1000 atoms: 0.31 Number of scatterers: 27744 At special positions: 0 Unit cell: (128.139, 128.139, 149.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 4 15.00 Na 8 11.00 O 4864 8.00 N 4484 7.00 C 18248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 63.5% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.546A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.761A pdb=" N TYR A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.595A pdb=" N ILE A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.717A pdb=" N ARG A 359 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 360 " --> pdb=" O ILE A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 360' Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 375 " --> pdb=" O TRP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 409 removed outlier: 3.678A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 4.260A pdb=" N ASP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.852A pdb=" N ILE A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.939A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.522A pdb=" N LYS A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 626 removed outlier: 3.699A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.078A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 removed outlier: 3.591A pdb=" N GLU A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.767A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 696 Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.612A pdb=" N TYR A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 775 removed outlier: 3.757A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 806 removed outlier: 3.756A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 removed outlier: 3.552A pdb=" N TYR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 842 removed outlier: 3.542A pdb=" N ASP A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 879 removed outlier: 3.564A pdb=" N PHE A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 945 through 954 Processing helix chain 'A' and resid 955 through 970 removed outlier: 3.666A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.821A pdb=" N TRP A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.583A pdb=" N VAL A1006 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1059 removed outlier: 3.675A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A1056 " --> pdb=" O ASN A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1093 removed outlier: 3.881A pdb=" N LEU A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.546A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.761A pdb=" N TYR B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.596A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.716A pdb=" N ARG B 359 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 360 " --> pdb=" O ILE B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 375 " --> pdb=" O TRP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.679A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.261A pdb=" N ASP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 493 through 507 Processing helix chain 'B' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.852A pdb=" N ILE B 557 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.938A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.521A pdb=" N LYS B 590 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 626 removed outlier: 3.698A pdb=" N GLU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.077A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.592A pdb=" N GLU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.767A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 690 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 696 Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.613A pdb=" N TYR B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 775 removed outlier: 3.757A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 806 removed outlier: 3.756A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 803 " --> pdb=" O TYR B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 816 removed outlier: 3.553A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 842 removed outlier: 3.543A pdb=" N ASP B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 879 removed outlier: 3.563A pdb=" N PHE B 859 " --> pdb=" O ILE B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 945 through 954 Processing helix chain 'B' and resid 955 through 970 removed outlier: 3.666A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.822A pdb=" N TRP B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1006 removed outlier: 3.583A pdb=" N VAL B1006 " --> pdb=" O PHE B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1059 removed outlier: 3.675A pdb=" N VAL B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B1056 " --> pdb=" O ASN B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1093 removed outlier: 3.881A pdb=" N LEU B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B1090 " --> pdb=" O LEU B1086 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.546A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.760A pdb=" N TYR C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.595A pdb=" N ILE C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 343 through 348 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.717A pdb=" N ARG C 359 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 360 " --> pdb=" O ILE C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 375 " --> pdb=" O TRP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 395 through 409 removed outlier: 3.678A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 4.261A pdb=" N ASP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 493 through 507 Processing helix chain 'C' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 562 removed outlier: 3.851A pdb=" N ILE C 557 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.938A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.521A pdb=" N LYS C 590 " --> pdb=" O SER C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 626 removed outlier: 3.700A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 4.078A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 653 removed outlier: 3.591A pdb=" N GLU C 653 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 675 Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.767A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 690 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 696 Processing helix chain 'C' and resid 717 through 722 Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.612A pdb=" N TYR C 745 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 775 removed outlier: 3.757A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 806 removed outlier: 3.756A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 802 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 803 " --> pdb=" O TYR C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 816 removed outlier: 3.553A pdb=" N TYR C 816 " --> pdb=" O GLU C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 842 removed outlier: 3.542A pdb=" N ASP C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 879 removed outlier: 3.563A pdb=" N PHE C 859 " --> pdb=" O ILE C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 893 Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 945 through 954 Processing helix chain 'C' and resid 955 through 970 removed outlier: 3.666A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.821A pdb=" N TRP C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1006 removed outlier: 3.583A pdb=" N VAL C1006 " --> pdb=" O PHE C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1059 removed outlier: 3.675A pdb=" N VAL C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C1056 " --> pdb=" O ASN C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1093 removed outlier: 3.881A pdb=" N LEU C1085 " --> pdb=" O ASP C1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C1090 " --> pdb=" O LEU C1086 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 151 through 167 removed outlier: 3.545A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.760A pdb=" N TYR D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 removed outlier: 3.595A pdb=" N ILE D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 343 through 348 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.718A pdb=" N ARG D 359 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 360 " --> pdb=" O ILE D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 360' Processing helix chain 'D' and resid 361 through 376 removed outlier: 3.647A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 375 " --> pdb=" O TRP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 395 through 409 removed outlier: 3.677A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.953A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 removed outlier: 4.260A pdb=" N ASP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 493 through 507 Processing helix chain 'D' and resid 509 through 521 removed outlier: 3.502A pdb=" N PHE D 514 " --> pdb=" O ALA D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 562 removed outlier: 3.852A pdb=" N ILE D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 573 removed outlier: 3.939A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.521A pdb=" N LYS D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 626 removed outlier: 3.700A pdb=" N GLU D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 4.078A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 653 removed outlier: 3.592A pdb=" N GLU D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 675 Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.766A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 690 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 717 through 722 Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.613A pdb=" N TYR D 745 " --> pdb=" O LEU D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 775 removed outlier: 3.758A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 3.757A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 802 " --> pdb=" O PHE D 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 803 " --> pdb=" O TYR D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 816 removed outlier: 3.553A pdb=" N TYR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 842 removed outlier: 3.542A pdb=" N ASP D 825 " --> pdb=" O ILE D 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 848 removed outlier: 4.042A pdb=" N ILE D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 879 removed outlier: 3.564A pdb=" N PHE D 859 " --> pdb=" O ILE D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 893 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 955 through 970 removed outlier: 3.667A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.821A pdb=" N TRP D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1006 removed outlier: 3.582A pdb=" N VAL D1006 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 3.676A pdb=" N VAL D1048 " --> pdb=" O ALA D1044 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D1056 " --> pdb=" O ASN D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1093 removed outlier: 3.882A pdb=" N LEU D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.037A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP A 169 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 292 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.036A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP B 169 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 292 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.037A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP C 169 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 292 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 107 through 108 removed outlier: 6.037A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.524A pdb=" N TRP D 169 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 292 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3744 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: 5.28 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4332 1.31 - 1.43: 7953 1.43 - 1.56: 15822 1.56 - 1.69: 49 1.69 - 1.82: 220 Bond restraints: 28376 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.25e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.692 -0.360 2.00e-02 2.50e+03 3.23e+02 bond pdb=" CBF Y01 D1301 " pdb=" CBH Y01 D1301 " ideal model delta sigma weight residual 1.550 1.716 -0.166 2.00e-02 2.50e+03 6.86e+01 ... (remaining 28371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 37153 2.50 - 5.00: 943 5.00 - 7.50: 156 7.50 - 10.00: 52 10.00 - 12.50: 20 Bond angle restraints: 38324 Sorted by residual: angle pdb=" C THR C 681 " pdb=" N LYS C 682 " pdb=" CA LYS C 682 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C THR A 681 " pdb=" N LYS A 682 " pdb=" CA LYS A 682 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" C THR D 681 " pdb=" N LYS D 682 " pdb=" CA LYS D 682 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C THR B 681 " pdb=" N LYS B 682 " pdb=" CA LYS B 682 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" N PHE B1003 " pdb=" CA PHE B1003 " pdb=" C PHE B1003 " ideal model delta sigma weight residual 113.16 120.14 -6.98 1.42e+00 4.96e-01 2.42e+01 ... (remaining 38319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 15486 24.34 - 48.68: 1038 48.68 - 73.02: 96 73.02 - 97.36: 20 97.36 - 121.70: 4 Dihedral angle restraints: 16644 sinusoidal: 6876 harmonic: 9768 Sorted by residual: dihedral pdb=" CA ILE B 315 " pdb=" C ILE B 315 " pdb=" N PRO B 316 " pdb=" CA PRO B 316 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE D 315 " pdb=" C ILE D 315 " pdb=" N PRO D 316 " pdb=" CA PRO D 316 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE A 315 " pdb=" C ILE A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 16641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4001 0.096 - 0.191: 239 0.191 - 0.287: 18 0.287 - 0.382: 6 0.382 - 0.478: 4 Chirality restraints: 4268 Sorted by residual: chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CBI Y01 A1301 " pdb=" CAU Y01 A1301 " pdb=" CBE Y01 A1301 " pdb=" CBG Y01 A1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.46 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 4265 not shown) Planarity restraints: 4684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 132 " -0.047 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO D 133 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO A 133 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 132 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO B 133 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 ... (remaining 4681 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 448 2.67 - 3.23: 25582 3.23 - 3.79: 43144 3.79 - 4.34: 60724 4.34 - 4.90: 95861 Nonbonded interactions: 225759 Sorted by model distance: nonbonded pdb=" CG2 VAL C 768 " pdb=" CZ PHE C1003 " model vdw 2.114 3.760 nonbonded pdb=" CG2 VAL A 768 " pdb=" CZ PHE A1003 " model vdw 2.115 3.760 nonbonded pdb=" CG2 VAL B 768 " pdb=" CZ PHE B1003 " model vdw 2.115 3.760 nonbonded pdb=" CG2 VAL D 768 " pdb=" CZ PHE D1003 " model vdw 2.115 3.760 nonbonded pdb=" CD1 LEU D 769 " pdb=" CZ PHE D1003 " model vdw 2.177 3.760 ... (remaining 225754 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.750 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.010 0.360 28384 Z= 0.455 Angle : 1.006 12.498 38324 Z= 0.502 Chirality : 0.057 0.478 4268 Planarity : 0.007 0.072 4684 Dihedral : 15.853 121.697 10292 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % 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: -6.54 (0.09), residues: 3252 helix: -4.46 (0.04), residues: 2176 sheet: -2.72 (0.36), residues: 180 loop : -3.55 (0.16), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 105 TYR 0.020 0.002 TYR B 995 PHE 0.042 0.002 PHE D 295 TRP 0.016 0.002 TRP B 886 HIS 0.004 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.46 (28376) covalent geometry : angle 1.00551 / 0.50 (38324) hydrogen bonds : bond 0.28877 / 19.46 ( 1260) hydrogen bonds : angle 10.38782 / 7.13 ( 3744) Misc. bond : bond 0.00029 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 710 time to evaluate : 1.041 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: A 108 TYR cc_start: 0.6950 (p90) cc_final: 0.6563 (p90) REVERT: A 181 LYS cc_start: 0.8816 (ptmm) cc_final: 0.8556 (tttt) REVERT: A 267 LYS cc_start: 0.8383 (tttp) cc_final: 0.7939 (ttmm) REVERT: A 271 GLN cc_start: 0.7347 (mt0) cc_final: 0.6693 (mt0) REVERT: A 286 TYR cc_start: 0.8664 (t80) cc_final: 0.7602 (t80) REVERT: A 304 LEU cc_start: 0.8296 (tp) cc_final: 0.8060 (tp) REVERT: A 359 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7520 (mtm110) REVERT: A 606 GLU cc_start: 0.8153 (tp30) cc_final: 0.7702 (tp30) REVERT: A 745 TYR cc_start: 0.7401 (t80) cc_final: 0.7066 (t80) REVERT: A 776 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 876 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 958 ASN cc_start: 0.9237 (t0) cc_final: 0.8966 (t0) REVERT: B 286 TYR cc_start: 0.8717 (t80) cc_final: 0.7720 (t80) REVERT: B 301 LYS cc_start: 0.8531 (tmmt) cc_final: 0.7939 (tptt) REVERT: B 328 ASP cc_start: 0.8144 (t70) cc_final: 0.7714 (t70) REVERT: B 606 GLU cc_start: 0.8197 (tp30) cc_final: 0.7813 (tp30) REVERT: B 745 TYR cc_start: 0.7289 (t80) cc_final: 0.7021 (t80) REVERT: B 776 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7759 (tm-30) REVERT: C 301 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8021 (tptt) REVERT: C 745 TYR cc_start: 0.7259 (t80) cc_final: 0.6671 (t80) REVERT: C 776 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 177 TYR cc_start: 0.7504 (m-80) cc_final: 0.7140 (m-80) REVERT: D 301 LYS cc_start: 0.8257 (tmmt) cc_final: 0.7961 (tptt) REVERT: D 552 LEU cc_start: 0.9059 (mt) cc_final: 0.8833 (mt) REVERT: D 776 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7595 (tm-30) REVERT: D 876 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7362 (tm-30) outliers start: 0 outliers final: 0 residues processed: 710 average time/residue: 0.1954 time to fit residues: 215.4651 Evaluate side-chains 534 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.3980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS A 271 GLN A 418 ASN A 471 ASN A 574 GLN A 597 ASN A1058 ASN ** A1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 428 ASN B 474 ASN B 553 GLN B 574 GLN B 597 ASN B1058 ASN C 126 GLN C 297 GLN C 418 ASN C 474 ASN C 553 GLN C 574 GLN C 597 ASN C 610 ASN C1058 ASN D 271 GLN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 574 GLN D 597 ASN D 610 ASN D 835 HIS D1058 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.173929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129521 restraints weight = 34560.879| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.49 r_work: 0.3338 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28384 Z= 0.126 Angle : 0.614 9.235 38324 Z= 0.322 Chirality : 0.042 0.173 4268 Planarity : 0.005 0.058 4684 Dihedral : 9.422 87.946 3820 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.81 % Allowed : 15.31 % Favored : 83.88 % 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: -4.11 (0.12), residues: 3252 helix: -2.30 (0.09), residues: 2216 sheet: -2.53 (0.38), residues: 176 loop : -3.37 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1071 TYR 0.020 0.001 TYR A 971 PHE 0.022 0.001 PHE C 497 TRP 0.012 0.001 TRP A 371 HIS 0.002 0.000 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (28376) covalent geometry : angle 0.61422 / 0.32 (38324) hydrogen bonds : bond 0.04179 / 2.80 ( 1260) hydrogen bonds : angle 4.81514 / 3.33 ( 3744) Misc. bond : bond 0.00036 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 612 time to evaluate : 0.941 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: A 108 TYR cc_start: 0.6948 (p90) cc_final: 0.6503 (p90) REVERT: A 267 LYS cc_start: 0.8295 (tttp) cc_final: 0.7891 (ttmm) REVERT: A 271 GLN cc_start: 0.7842 (mt0) cc_final: 0.7412 (mt0) REVERT: A 286 TYR cc_start: 0.8498 (t80) cc_final: 0.7483 (t80) REVERT: A 304 LEU cc_start: 0.8036 (tp) cc_final: 0.7788 (tp) REVERT: A 355 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7380 (mtm-85) REVERT: A 359 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7593 (mtt90) REVERT: A 613 GLU cc_start: 0.8104 (tt0) cc_final: 0.7792 (tt0) REVERT: A 745 TYR cc_start: 0.7983 (t80) cc_final: 0.7775 (t80) REVERT: A 771 CYS cc_start: 0.8542 (t) cc_final: 0.8264 (t) REVERT: A 776 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 876 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 180 MET cc_start: 0.8709 (mtm) cc_final: 0.8314 (mtm) REVERT: B 286 TYR cc_start: 0.8457 (t80) cc_final: 0.7470 (t80) REVERT: B 301 LYS cc_start: 0.8255 (tmmt) cc_final: 0.7693 (tttt) REVERT: B 613 GLU cc_start: 0.8125 (tt0) cc_final: 0.7826 (tt0) REVERT: B 771 CYS cc_start: 0.8451 (t) cc_final: 0.8129 (t) REVERT: B 776 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 876 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7844 (tm-30) REVERT: B 969 PHE cc_start: 0.8813 (m-80) cc_final: 0.8574 (m-80) REVERT: B 1056 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8355 (mmtp) REVERT: C 286 TYR cc_start: 0.8456 (t80) cc_final: 0.7508 (t80) REVERT: C 301 LYS cc_start: 0.8408 (tmmt) cc_final: 0.7845 (tttt) REVERT: C 749 MET cc_start: 0.7686 (mmt) cc_final: 0.7401 (mmt) REVERT: C 771 CYS cc_start: 0.8378 (t) cc_final: 0.8009 (t) REVERT: C 776 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 177 TYR cc_start: 0.7509 (m-80) cc_final: 0.7236 (m-80) REVERT: D 301 LYS cc_start: 0.8115 (tmmt) cc_final: 0.7435 (tttp) REVERT: D 321 GLU cc_start: 0.8354 (pm20) cc_final: 0.8064 (pm20) REVERT: D 431 ASP cc_start: 0.8291 (p0) cc_final: 0.8054 (p0) REVERT: D 771 CYS cc_start: 0.8466 (t) cc_final: 0.8181 (t) REVERT: D 776 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8003 (tm-30) outliers start: 24 outliers final: 10 residues processed: 625 average time/residue: 0.1791 time to fit residues: 179.6136 Evaluate side-chains 538 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 528 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 825 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 317 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 66 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 HIS A 428 ASN A 553 GLN B 248 HIS B 553 GLN ** B 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 297 GLN ** C 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 248 HIS D 474 ASN D 553 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.177220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133312 restraints weight = 34150.208| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.53 r_work: 0.3198 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28384 Z= 0.146 Angle : 0.613 10.494 38324 Z= 0.313 Chirality : 0.042 0.226 4268 Planarity : 0.004 0.056 4684 Dihedral : 8.756 74.026 3820 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.62 % Allowed : 18.37 % Favored : 80.01 % 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: -2.73 (0.13), residues: 3252 helix: -1.09 (0.10), residues: 2192 sheet: -2.80 (0.44), residues: 140 loop : -3.13 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 615 TYR 0.021 0.001 TYR D 971 PHE 0.016 0.001 PHE D 295 TRP 0.013 0.001 TRP B 371 HIS 0.002 0.000 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (28376) covalent geometry : angle 0.61280 / 0.31 (38324) hydrogen bonds : bond 0.03806 / 2.53 ( 1260) hydrogen bonds : angle 4.28506 / 2.97 ( 3744) Misc. bond : bond 0.00049 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 572 time to evaluate : 0.983 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: A 108 TYR cc_start: 0.6965 (p90) cc_final: 0.6480 (p90) REVERT: A 286 TYR cc_start: 0.8485 (t80) cc_final: 0.7435 (t80) REVERT: A 355 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: A 359 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7575 (mtm110) REVERT: A 606 GLU cc_start: 0.8589 (tp30) cc_final: 0.8170 (tp30) REVERT: A 613 GLU cc_start: 0.8285 (tt0) cc_final: 0.7917 (tt0) REVERT: A 745 TYR cc_start: 0.7959 (t80) cc_final: 0.7722 (t80) REVERT: A 771 CYS cc_start: 0.8695 (t) cc_final: 0.8418 (t) REVERT: A 776 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 1056 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8308 (mmtp) REVERT: B 180 MET cc_start: 0.8666 (mtm) cc_final: 0.8378 (mtm) REVERT: B 301 LYS cc_start: 0.8292 (tmmt) cc_final: 0.7723 (tptt) REVERT: B 436 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 613 GLU cc_start: 0.8306 (tt0) cc_final: 0.7924 (tt0) REVERT: B 695 LEU cc_start: 0.8630 (mt) cc_final: 0.8406 (mt) REVERT: B 745 TYR cc_start: 0.7915 (t80) cc_final: 0.7384 (t80) REVERT: B 769 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7728 (mp) REVERT: B 771 CYS cc_start: 0.8680 (t) cc_final: 0.8347 (t) REVERT: B 776 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 1056 LYS cc_start: 0.8546 (mmtp) cc_final: 0.8336 (mmtp) REVERT: C 180 MET cc_start: 0.8550 (mtm) cc_final: 0.8312 (mtm) REVERT: C 301 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7731 (tptt) REVERT: C 305 LYS cc_start: 0.8111 (ptpt) cc_final: 0.7603 (tptt) REVERT: C 700 PHE cc_start: 0.7443 (t80) cc_final: 0.7163 (t80) REVERT: C 749 MET cc_start: 0.7712 (mmt) cc_final: 0.7056 (mmp) REVERT: C 771 CYS cc_start: 0.8559 (t) cc_final: 0.8155 (t) REVERT: C 776 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 177 TYR cc_start: 0.7667 (m-80) cc_final: 0.7345 (m-80) REVERT: D 305 LYS cc_start: 0.7575 (ptpp) cc_final: 0.7371 (tptp) REVERT: D 700 PHE cc_start: 0.7379 (t80) cc_final: 0.6999 (t80) REVERT: D 771 CYS cc_start: 0.8645 (t) cc_final: 0.8329 (t) REVERT: D 776 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7355 (tm-30) REVERT: D 784 TYR cc_start: 0.7049 (t80) cc_final: 0.6614 (t80) REVERT: D 790 ASN cc_start: 0.8277 (t0) cc_final: 0.7946 (t0) REVERT: D 825 ASP cc_start: 0.8532 (t70) cc_final: 0.7982 (t70) REVERT: D 876 GLN cc_start: 0.8610 (tp40) cc_final: 0.8103 (tm-30) outliers start: 48 outliers final: 24 residues processed: 598 average time/residue: 0.1866 time to fit residues: 179.3175 Evaluate side-chains 550 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 525 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 849 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 190 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 HIS B 550 HIS B 835 HIS C 126 GLN C 297 GLN C 501 GLN C 550 HIS C 835 HIS ** C1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 471 ASN D 550 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.179386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136026 restraints weight = 33737.122| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.48 r_work: 0.3225 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28384 Z= 0.129 Angle : 0.577 9.564 38324 Z= 0.295 Chirality : 0.042 0.172 4268 Planarity : 0.004 0.053 4684 Dihedral : 8.264 63.397 3820 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.51 % Allowed : 20.15 % Favored : 78.33 % 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: -2.09 (0.14), residues: 3252 helix: -0.54 (0.11), residues: 2212 sheet: -2.71 (0.44), residues: 140 loop : -3.11 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 523 TYR 0.022 0.001 TYR B 286 PHE 0.014 0.001 PHE B 969 TRP 0.014 0.001 TRP A 371 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (28376) covalent geometry : angle 0.57712 / 0.30 (38324) hydrogen bonds : bond 0.03362 / 2.24 ( 1260) hydrogen bonds : angle 4.00030 / 2.78 ( 3744) Misc. bond : bond 0.00047 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 561 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7064 (p90) cc_final: 0.6483 (p90) REVERT: A 286 TYR cc_start: 0.8467 (t80) cc_final: 0.7508 (t80) REVERT: A 387 ILE cc_start: 0.8113 (mp) cc_final: 0.7862 (mm) REVERT: A 494 SER cc_start: 0.8741 (m) cc_final: 0.8261 (p) REVERT: A 613 GLU cc_start: 0.8200 (tt0) cc_final: 0.7953 (tt0) REVERT: A 745 TYR cc_start: 0.7943 (t80) cc_final: 0.7731 (t80) REVERT: A 773 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 776 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 164 GLN cc_start: 0.8650 (tp40) cc_final: 0.7997 (tp40) REVERT: B 301 LYS cc_start: 0.8313 (tmmt) cc_final: 0.7629 (tptt) REVERT: B 305 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7784 (tptt) REVERT: B 387 ILE cc_start: 0.8022 (mp) cc_final: 0.7756 (mm) REVERT: B 494 SER cc_start: 0.8715 (m) cc_final: 0.8205 (p) REVERT: B 613 GLU cc_start: 0.8257 (tt0) cc_final: 0.7881 (tt0) REVERT: B 768 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 769 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7411 (mp) REVERT: B 771 CYS cc_start: 0.8709 (t) cc_final: 0.8396 (t) REVERT: B 773 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8328 (mm-30) REVERT: B 776 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 876 GLN cc_start: 0.8542 (tp40) cc_final: 0.8117 (tm-30) REVERT: C 301 LYS cc_start: 0.8386 (tmmt) cc_final: 0.7721 (tptt) REVERT: C 305 LYS cc_start: 0.8042 (ptpt) cc_final: 0.7660 (tptt) REVERT: C 494 SER cc_start: 0.8863 (m) cc_final: 0.8351 (p) REVERT: C 749 MET cc_start: 0.7741 (mmt) cc_final: 0.7113 (mmp) REVERT: C 769 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7248 (mp) REVERT: C 771 CYS cc_start: 0.8595 (t) cc_final: 0.8179 (t) REVERT: C 773 GLU cc_start: 0.8726 (tp30) cc_final: 0.8453 (tp30) REVERT: C 1068 MET cc_start: 0.5801 (mtp) cc_final: 0.5562 (mpp) REVERT: D 177 TYR cc_start: 0.7649 (m-80) cc_final: 0.7363 (m-80) REVERT: D 494 SER cc_start: 0.8763 (m) cc_final: 0.8206 (p) REVERT: D 771 CYS cc_start: 0.8674 (t) cc_final: 0.8395 (t) REVERT: D 773 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8218 (mm-30) REVERT: D 776 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7405 (tm-30) REVERT: D 784 TYR cc_start: 0.7310 (t80) cc_final: 0.6811 (t80) REVERT: D 790 ASN cc_start: 0.8254 (t0) cc_final: 0.7966 (t0) REVERT: D 876 GLN cc_start: 0.8637 (tp40) cc_final: 0.8164 (tm-30) REVERT: D 1075 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7233 (tt) outliers start: 45 outliers final: 29 residues processed: 589 average time/residue: 0.1873 time to fit residues: 176.4209 Evaluate side-chains 540 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 507 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 156 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 319 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 205 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 297 GLN D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.178562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134829 restraints weight = 33916.608| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.52 r_work: 0.3305 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28384 Z= 0.124 Angle : 0.568 8.801 38324 Z= 0.290 Chirality : 0.041 0.181 4268 Planarity : 0.004 0.050 4684 Dihedral : 8.014 59.576 3820 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.88 % Allowed : 20.73 % Favored : 77.39 % 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 (0.14), residues: 3252 helix: -0.25 (0.11), residues: 2216 sheet: -2.61 (0.45), residues: 140 loop : -3.00 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 153 TYR 0.029 0.001 TYR B 286 PHE 0.017 0.001 PHE D 969 TRP 0.011 0.001 TRP C 371 HIS 0.002 0.000 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (28376) covalent geometry : angle 0.56799 / 0.29 (38324) hydrogen bonds : bond 0.03282 / 2.19 ( 1260) hydrogen bonds : angle 3.87642 / 2.69 ( 3744) Misc. bond : bond 0.00043 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 551 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7079 (p90) cc_final: 0.6522 (p90) REVERT: A 164 GLN cc_start: 0.8533 (tp40) cc_final: 0.7773 (tt0) REVERT: A 286 TYR cc_start: 0.8469 (t80) cc_final: 0.7616 (t80) REVERT: A 387 ILE cc_start: 0.8088 (mp) cc_final: 0.7843 (mm) REVERT: A 494 SER cc_start: 0.8733 (m) cc_final: 0.8268 (p) REVERT: A 613 GLU cc_start: 0.8210 (tt0) cc_final: 0.7925 (tt0) REVERT: A 745 TYR cc_start: 0.7935 (t80) cc_final: 0.7424 (t80) REVERT: A 773 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 776 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 1075 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 164 GLN cc_start: 0.8616 (tp40) cc_final: 0.7955 (tp40) REVERT: B 301 LYS cc_start: 0.8257 (tmmt) cc_final: 0.7581 (tptt) REVERT: B 305 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7801 (tptt) REVERT: B 494 SER cc_start: 0.8876 (m) cc_final: 0.8378 (p) REVERT: B 613 GLU cc_start: 0.8242 (tt0) cc_final: 0.7872 (tt0) REVERT: B 685 LYS cc_start: 0.8872 (mttp) cc_final: 0.8534 (tttm) REVERT: B 700 PHE cc_start: 0.7596 (t80) cc_final: 0.7180 (t80) REVERT: B 771 CYS cc_start: 0.8675 (t) cc_final: 0.8372 (t) REVERT: B 773 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 776 GLN cc_start: 0.8623 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 784 TYR cc_start: 0.7362 (t80) cc_final: 0.7123 (t80) REVERT: B 876 GLN cc_start: 0.8575 (tp40) cc_final: 0.8154 (tm-30) REVERT: B 1075 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7488 (tt) REVERT: C 301 LYS cc_start: 0.8373 (tmmt) cc_final: 0.7671 (tttp) REVERT: C 305 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7667 (tptt) REVERT: C 321 GLU cc_start: 0.8535 (pm20) cc_final: 0.8120 (pm20) REVERT: C 494 SER cc_start: 0.8804 (m) cc_final: 0.8321 (p) REVERT: C 613 GLU cc_start: 0.8158 (tt0) cc_final: 0.7888 (tt0) REVERT: C 749 MET cc_start: 0.7796 (mmt) cc_final: 0.7156 (mmp) REVERT: C 771 CYS cc_start: 0.8689 (t) cc_final: 0.8308 (t) REVERT: C 776 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 1075 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7469 (tt) REVERT: D 177 TYR cc_start: 0.7656 (m-80) cc_final: 0.7420 (m-80) REVERT: D 494 SER cc_start: 0.8827 (m) cc_final: 0.8307 (p) REVERT: D 771 CYS cc_start: 0.8663 (t) cc_final: 0.8417 (t) REVERT: D 773 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 776 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 784 TYR cc_start: 0.7344 (t80) cc_final: 0.6867 (t80) REVERT: D 790 ASN cc_start: 0.8216 (t0) cc_final: 0.7882 (t0) REVERT: D 876 GLN cc_start: 0.8644 (tp40) cc_final: 0.8166 (tm-30) REVERT: D 1075 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7115 (tt) outliers start: 56 outliers final: 38 residues processed: 585 average time/residue: 0.1846 time to fit residues: 174.2459 Evaluate side-chains 550 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 508 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 778 TYR Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 767 PHE Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 68 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 328 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN A 835 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN C 126 GLN C 297 GLN C 410 ASN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 790 ASN D 126 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.181764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138051 restraints weight = 33635.587| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.53 r_work: 0.3206 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28384 Z= 0.134 Angle : 0.568 11.202 38324 Z= 0.291 Chirality : 0.042 0.154 4268 Planarity : 0.004 0.047 4684 Dihedral : 7.869 59.905 3820 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.39 % Allowed : 20.76 % Favored : 76.85 % 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: -1.54 (0.15), residues: 3252 helix: -0.08 (0.11), residues: 2216 sheet: -2.64 (0.46), residues: 140 loop : -3.01 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 153 TYR 0.032 0.001 TYR D 286 PHE 0.016 0.001 PHE D 969 TRP 0.014 0.001 TRP D 371 HIS 0.002 0.000 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (28376) covalent geometry : angle 0.56797 / 0.29 (38324) hydrogen bonds : bond 0.03238 / 2.16 ( 1260) hydrogen bonds : angle 3.82877 / 2.66 ( 3744) Misc. bond : bond 0.00040 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 551 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.8556 (tp40) cc_final: 0.7792 (tt0) REVERT: A 286 TYR cc_start: 0.8476 (t80) cc_final: 0.7725 (t80) REVERT: A 297 GLN cc_start: 0.7874 (pm20) cc_final: 0.7305 (pm20) REVERT: A 494 SER cc_start: 0.8740 (m) cc_final: 0.8250 (p) REVERT: A 606 GLU cc_start: 0.8594 (tp30) cc_final: 0.8174 (tp30) REVERT: A 613 GLU cc_start: 0.8253 (tt0) cc_final: 0.7877 (tt0) REVERT: A 776 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 876 GLN cc_start: 0.8610 (tp40) cc_final: 0.8033 (tm-30) REVERT: A 1075 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 164 GLN cc_start: 0.8650 (tp40) cc_final: 0.7822 (tt0) REVERT: B 301 LYS cc_start: 0.8222 (tmmt) cc_final: 0.7530 (tptt) REVERT: B 305 LYS cc_start: 0.8078 (ptpt) cc_final: 0.7764 (tptt) REVERT: B 387 ILE cc_start: 0.8009 (mp) cc_final: 0.7643 (mt) REVERT: B 494 SER cc_start: 0.8865 (m) cc_final: 0.8355 (p) REVERT: B 613 GLU cc_start: 0.8239 (tt0) cc_final: 0.7821 (tt0) REVERT: B 768 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 769 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 771 CYS cc_start: 0.8700 (t) cc_final: 0.8390 (t) REVERT: B 773 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8206 (mm-30) REVERT: B 776 GLN cc_start: 0.8634 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 784 TYR cc_start: 0.7327 (t80) cc_final: 0.7000 (t80) REVERT: B 876 GLN cc_start: 0.8567 (tp40) cc_final: 0.8119 (tm-30) REVERT: B 1075 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7798 (mp) REVERT: C 297 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7042 (pp30) REVERT: C 301 LYS cc_start: 0.8316 (tmmt) cc_final: 0.7553 (tptt) REVERT: C 305 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7687 (tptt) REVERT: C 321 GLU cc_start: 0.8586 (pm20) cc_final: 0.8150 (pm20) REVERT: C 494 SER cc_start: 0.8836 (m) cc_final: 0.8345 (p) REVERT: C 557 ILE cc_start: 0.9135 (mt) cc_final: 0.8891 (mt) REVERT: C 613 GLU cc_start: 0.8096 (tt0) cc_final: 0.7834 (tt0) REVERT: C 749 MET cc_start: 0.7794 (mmt) cc_final: 0.7134 (mmp) REVERT: C 771 CYS cc_start: 0.8759 (t) cc_final: 0.8379 (t) REVERT: C 1068 MET cc_start: 0.4190 (mpp) cc_final: 0.3827 (mtp) REVERT: C 1085 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4951 (tt) REVERT: D 436 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 494 SER cc_start: 0.8813 (m) cc_final: 0.8302 (p) REVERT: D 771 CYS cc_start: 0.8729 (t) cc_final: 0.8454 (t) REVERT: D 776 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 784 TYR cc_start: 0.7438 (t80) cc_final: 0.7092 (t80) REVERT: D 790 ASN cc_start: 0.8261 (t0) cc_final: 0.7781 (t0) outliers start: 71 outliers final: 50 residues processed: 598 average time/residue: 0.1826 time to fit residues: 176.5202 Evaluate side-chains 558 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 502 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 700 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 1046 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 52 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 284 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 250 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 410 ASN C 501 GLN C 550 HIS D 126 GLN D 553 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.180646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137045 restraints weight = 33664.076| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.53 r_work: 0.3249 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28384 Z= 0.129 Angle : 0.576 9.439 38324 Z= 0.294 Chirality : 0.042 0.201 4268 Planarity : 0.004 0.047 4684 Dihedral : 7.691 58.841 3820 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.49 % Allowed : 20.73 % Favored : 76.78 % 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: -1.39 (0.15), residues: 3252 helix: 0.05 (0.11), residues: 2212 sheet: -2.61 (0.46), residues: 140 loop : -2.99 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.033 0.001 TYR D 286 PHE 0.018 0.001 PHE B 858 TRP 0.013 0.001 TRP D 371 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (28376) covalent geometry : angle 0.57595 / 0.29 (38324) hydrogen bonds : bond 0.03186 / 2.13 ( 1260) hydrogen bonds : angle 3.77995 / 2.63 ( 3744) Misc. bond : bond 0.00035 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 536 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7195 (p90) cc_final: 0.6626 (p90) REVERT: A 286 TYR cc_start: 0.8487 (t80) cc_final: 0.7858 (t80) REVERT: A 297 GLN cc_start: 0.7833 (pm20) cc_final: 0.7286 (pm20) REVERT: A 494 SER cc_start: 0.8762 (m) cc_final: 0.8273 (p) REVERT: A 501 GLN cc_start: 0.7323 (tp40) cc_final: 0.7092 (mm110) REVERT: A 613 GLU cc_start: 0.8198 (tt0) cc_final: 0.7809 (tt0) REVERT: A 776 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 784 TYR cc_start: 0.7771 (t80) cc_final: 0.7417 (t80) REVERT: A 876 GLN cc_start: 0.8599 (tp40) cc_final: 0.8022 (tm-30) REVERT: A 1068 MET cc_start: 0.5355 (mtp) cc_final: 0.5029 (mpp) REVERT: A 1075 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 164 GLN cc_start: 0.8655 (tp40) cc_final: 0.7845 (tt0) REVERT: B 301 LYS cc_start: 0.8264 (tmmt) cc_final: 0.7580 (tptt) REVERT: B 305 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7760 (tptt) REVERT: B 387 ILE cc_start: 0.8032 (mp) cc_final: 0.7658 (mt) REVERT: B 494 SER cc_start: 0.8853 (m) cc_final: 0.8346 (p) REVERT: B 613 GLU cc_start: 0.8207 (tt0) cc_final: 0.7985 (tt0) REVERT: B 769 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7189 (mp) REVERT: B 773 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8222 (mm-30) REVERT: B 776 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 876 GLN cc_start: 0.8624 (tp40) cc_final: 0.8156 (tm-30) REVERT: B 1075 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7757 (mp) REVERT: C 130 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 154 LYS cc_start: 0.8979 (tttm) cc_final: 0.8321 (mttp) REVERT: C 301 LYS cc_start: 0.8343 (tmmt) cc_final: 0.7699 (tttt) REVERT: C 305 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7695 (tptt) REVERT: C 321 GLU cc_start: 0.8516 (pm20) cc_final: 0.8114 (pm20) REVERT: C 364 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6161 (pt0) REVERT: C 494 SER cc_start: 0.8823 (m) cc_final: 0.8333 (p) REVERT: C 557 ILE cc_start: 0.9114 (mt) cc_final: 0.8871 (mt) REVERT: C 613 GLU cc_start: 0.8078 (tt0) cc_final: 0.7798 (tt0) REVERT: C 685 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8777 (tttp) REVERT: C 749 MET cc_start: 0.7782 (mmt) cc_final: 0.7135 (mmp) REVERT: C 771 CYS cc_start: 0.8839 (t) cc_final: 0.8476 (t) REVERT: C 876 GLN cc_start: 0.8629 (tp40) cc_final: 0.8282 (tm-30) REVERT: C 1075 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7375 (tp) REVERT: C 1085 LEU cc_start: 0.5218 (OUTLIER) cc_final: 0.4921 (tt) REVERT: D 452 VAL cc_start: 0.8709 (p) cc_final: 0.8467 (t) REVERT: D 494 SER cc_start: 0.8789 (m) cc_final: 0.8286 (p) REVERT: D 771 CYS cc_start: 0.8760 (t) cc_final: 0.8518 (t) REVERT: D 776 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 784 TYR cc_start: 0.7343 (t80) cc_final: 0.7120 (t80) REVERT: D 790 ASN cc_start: 0.8257 (t0) cc_final: 0.7793 (t0) REVERT: D 876 GLN cc_start: 0.8618 (tp40) cc_final: 0.8053 (tm-30) REVERT: D 1075 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7152 (tt) outliers start: 74 outliers final: 56 residues processed: 585 average time/residue: 0.1835 time to fit residues: 174.3838 Evaluate side-chains 576 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 512 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 700 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 328 optimal weight: 0.3980 chunk 139 optimal weight: 0.0040 chunk 316 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 175 optimal weight: 6.9990 chunk 127 optimal weight: 0.0010 chunk 258 optimal weight: 0.8980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN B 271 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 297 GLN C 410 ASN C 550 HIS D 126 GLN D 553 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.184517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141347 restraints weight = 33680.096| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.55 r_work: 0.3271 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28384 Z= 0.101 Angle : 0.554 9.049 38324 Z= 0.283 Chirality : 0.041 0.208 4268 Planarity : 0.004 0.049 4684 Dihedral : 7.363 58.271 3820 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.99 % Allowed : 21.53 % Favored : 76.48 % 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: -1.10 (0.15), residues: 3252 helix: 0.27 (0.11), residues: 2200 sheet: -2.56 (0.47), residues: 136 loop : -2.85 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1071 TYR 0.048 0.001 TYR C 286 PHE 0.018 0.001 PHE D 858 TRP 0.019 0.001 TRP C 684 HIS 0.007 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (28376) covalent geometry : angle 0.55400 / 0.28 (38324) hydrogen bonds : bond 0.03018 / 2.02 ( 1260) hydrogen bonds : angle 3.66699 / 2.54 ( 3744) Misc. bond : bond 0.00043 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 575 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7080 (p90) cc_final: 0.6502 (p90) REVERT: A 164 GLN cc_start: 0.8654 (tp40) cc_final: 0.8295 (tt0) REVERT: A 297 GLN cc_start: 0.7759 (pm20) cc_final: 0.7291 (pm20) REVERT: A 387 ILE cc_start: 0.8007 (mp) cc_final: 0.7764 (mm) REVERT: A 494 SER cc_start: 0.8707 (m) cc_final: 0.8259 (p) REVERT: A 613 GLU cc_start: 0.8098 (tt0) cc_final: 0.7811 (tt0) REVERT: A 776 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 784 TYR cc_start: 0.7841 (t80) cc_final: 0.7290 (t80) REVERT: A 1075 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7798 (mp) REVERT: B 164 GLN cc_start: 0.8656 (tp40) cc_final: 0.7795 (tt0) REVERT: B 271 GLN cc_start: 0.7506 (mt0) cc_final: 0.7263 (tm-30) REVERT: B 301 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7508 (tptt) REVERT: B 305 LYS cc_start: 0.7908 (ptpt) cc_final: 0.7649 (tptt) REVERT: B 363 GLU cc_start: 0.7860 (pp20) cc_final: 0.7543 (mm-30) REVERT: B 387 ILE cc_start: 0.8017 (mp) cc_final: 0.7644 (mt) REVERT: B 494 SER cc_start: 0.8780 (m) cc_final: 0.8297 (p) REVERT: B 613 GLU cc_start: 0.8118 (tt0) cc_final: 0.7837 (tt0) REVERT: B 768 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 769 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7099 (mp) REVERT: B 773 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 776 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 876 GLN cc_start: 0.8619 (tp40) cc_final: 0.8127 (tm-30) REVERT: B 1075 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7704 (mp) REVERT: C 154 LYS cc_start: 0.8887 (tttm) cc_final: 0.8159 (mttp) REVERT: C 301 LYS cc_start: 0.8308 (tmmt) cc_final: 0.7645 (tttp) REVERT: C 305 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7608 (tptt) REVERT: C 321 GLU cc_start: 0.8497 (pm20) cc_final: 0.8119 (pm20) REVERT: C 387 ILE cc_start: 0.7942 (mp) cc_final: 0.7556 (mt) REVERT: C 494 SER cc_start: 0.8865 (m) cc_final: 0.8369 (p) REVERT: C 557 ILE cc_start: 0.9116 (mt) cc_final: 0.8833 (mt) REVERT: C 613 GLU cc_start: 0.7945 (tt0) cc_final: 0.7643 (tt0) REVERT: C 749 MET cc_start: 0.7774 (mmt) cc_final: 0.7122 (mmp) REVERT: C 771 CYS cc_start: 0.8838 (t) cc_final: 0.8482 (t) REVERT: C 1075 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7643 (mp) REVERT: D 154 LYS cc_start: 0.8895 (tttm) cc_final: 0.8274 (mttp) REVERT: D 387 ILE cc_start: 0.7981 (mp) cc_final: 0.7575 (mt) REVERT: D 494 SER cc_start: 0.8816 (m) cc_final: 0.8338 (p) REVERT: D 771 CYS cc_start: 0.8724 (t) cc_final: 0.8499 (t) REVERT: D 776 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7931 (tm-30) REVERT: D 784 TYR cc_start: 0.7626 (t80) cc_final: 0.7262 (t80) REVERT: D 790 ASN cc_start: 0.8112 (t0) cc_final: 0.7683 (t0) REVERT: D 1075 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7366 (mm) outliers start: 59 outliers final: 38 residues processed: 619 average time/residue: 0.1846 time to fit residues: 185.2592 Evaluate side-chains 571 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 527 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 658 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 658 GLN C 126 GLN C 412 HIS C 550 HIS D 126 GLN D 145 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.180843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138064 restraints weight = 33734.629| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.47 r_work: 0.3353 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28384 Z= 0.132 Angle : 0.600 11.204 38324 Z= 0.303 Chirality : 0.042 0.212 4268 Planarity : 0.004 0.047 4684 Dihedral : 7.378 58.490 3820 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.05 % Allowed : 21.77 % Favored : 76.18 % 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 (0.15), residues: 3252 helix: 0.32 (0.11), residues: 2200 sheet: -2.49 (0.46), residues: 140 loop : -2.85 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1071 TYR 0.051 0.002 TYR B 286 PHE 0.017 0.001 PHE D 969 TRP 0.013 0.001 TRP C 684 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (28376) covalent geometry : angle 0.59982 / 0.30 (38324) hydrogen bonds : bond 0.03168 / 2.12 ( 1260) hydrogen bonds : angle 3.69410 / 2.57 ( 3744) Misc. bond : bond 0.00031 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 538 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.8566 (tp40) cc_final: 0.7800 (tt0) REVERT: A 297 GLN cc_start: 0.7835 (pm20) cc_final: 0.7386 (pm20) REVERT: A 387 ILE cc_start: 0.8061 (mp) cc_final: 0.7714 (mt) REVERT: A 494 SER cc_start: 0.8722 (m) cc_final: 0.8278 (p) REVERT: A 613 GLU cc_start: 0.8147 (tt0) cc_final: 0.7820 (tt0) REVERT: A 776 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 784 TYR cc_start: 0.7605 (t80) cc_final: 0.7164 (t80) REVERT: A 1075 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7845 (mp) REVERT: B 164 GLN cc_start: 0.8652 (tp40) cc_final: 0.7825 (tt0) REVERT: B 301 LYS cc_start: 0.8313 (tmmt) cc_final: 0.7697 (tttp) REVERT: B 305 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7696 (tptt) REVERT: B 387 ILE cc_start: 0.8058 (mp) cc_final: 0.7687 (mt) REVERT: B 494 SER cc_start: 0.8768 (m) cc_final: 0.8306 (p) REVERT: B 613 GLU cc_start: 0.8156 (tt0) cc_final: 0.7851 (tt0) REVERT: B 768 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 773 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8229 (mm-30) REVERT: B 776 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 876 GLN cc_start: 0.8659 (tp40) cc_final: 0.8179 (tm-30) REVERT: B 1075 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7658 (mp) REVERT: C 154 LYS cc_start: 0.8930 (tttm) cc_final: 0.8241 (mttp) REVERT: C 301 LYS cc_start: 0.8372 (tmmt) cc_final: 0.7694 (tttp) REVERT: C 305 LYS cc_start: 0.7947 (ptpt) cc_final: 0.7671 (tptt) REVERT: C 321 GLU cc_start: 0.8479 (pm20) cc_final: 0.8112 (pm20) REVERT: C 364 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5436 (pm20) REVERT: C 387 ILE cc_start: 0.8025 (mp) cc_final: 0.7629 (mt) REVERT: C 494 SER cc_start: 0.8868 (m) cc_final: 0.8398 (p) REVERT: C 557 ILE cc_start: 0.9129 (mt) cc_final: 0.8848 (mt) REVERT: C 613 GLU cc_start: 0.8021 (tt0) cc_final: 0.7721 (tt0) REVERT: C 749 MET cc_start: 0.7794 (mmt) cc_final: 0.7182 (mmp) REVERT: C 771 CYS cc_start: 0.8808 (t) cc_final: 0.8478 (t) REVERT: C 1075 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7624 (mp) REVERT: D 154 LYS cc_start: 0.8966 (tttm) cc_final: 0.8355 (mttp) REVERT: D 494 SER cc_start: 0.8841 (m) cc_final: 0.8354 (p) REVERT: D 771 CYS cc_start: 0.8669 (t) cc_final: 0.8468 (t) REVERT: D 776 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7931 (tm-30) REVERT: D 784 TYR cc_start: 0.7596 (t80) cc_final: 0.7295 (t80) REVERT: D 790 ASN cc_start: 0.8135 (t0) cc_final: 0.7847 (t0) REVERT: D 876 GLN cc_start: 0.8598 (tp40) cc_final: 0.8060 (tm-30) REVERT: D 1075 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7462 (mp) outliers start: 61 outliers final: 47 residues processed: 582 average time/residue: 0.1740 time to fit residues: 164.6651 Evaluate side-chains 565 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 512 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 700 PHE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 173 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 218 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN ** A 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 126 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.178523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135342 restraints weight = 33811.514| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.49 r_work: 0.3283 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28384 Z= 0.132 Angle : 0.602 11.497 38324 Z= 0.305 Chirality : 0.043 0.220 4268 Planarity : 0.004 0.048 4684 Dihedral : 7.363 59.961 3820 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.09 % Allowed : 21.67 % Favored : 76.24 % 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 (0.15), residues: 3252 helix: 0.31 (0.11), residues: 2208 sheet: -2.49 (0.45), residues: 140 loop : -2.86 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.047 0.002 TYR B 286 PHE 0.025 0.001 PHE C 858 TRP 0.031 0.001 TRP A 684 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (28376) covalent geometry : angle 0.60222 / 0.31 (38324) hydrogen bonds : bond 0.03163 / 2.12 ( 1260) hydrogen bonds : angle 3.71247 / 2.58 ( 3744) Misc. bond : bond 0.00034 / 0.02 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 527 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.8625 (tp40) cc_final: 0.7811 (tt0) REVERT: A 271 GLN cc_start: 0.7584 (mt0) cc_final: 0.7317 (tm-30) REVERT: A 387 ILE cc_start: 0.8048 (mp) cc_final: 0.7673 (mt) REVERT: A 494 SER cc_start: 0.8723 (m) cc_final: 0.8279 (p) REVERT: A 613 GLU cc_start: 0.8194 (tt0) cc_final: 0.7992 (tt0) REVERT: A 776 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 784 TYR cc_start: 0.7734 (t80) cc_final: 0.6653 (t80) REVERT: A 876 GLN cc_start: 0.8563 (tp40) cc_final: 0.8030 (tm-30) REVERT: A 1075 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7643 (mp) REVERT: B 164 GLN cc_start: 0.8662 (tp40) cc_final: 0.7826 (tt0) REVERT: B 271 GLN cc_start: 0.7530 (mt0) cc_final: 0.7302 (tm-30) REVERT: B 301 LYS cc_start: 0.8278 (tmmt) cc_final: 0.7642 (tptt) REVERT: B 305 LYS cc_start: 0.7951 (ptpt) cc_final: 0.7706 (tptt) REVERT: B 363 GLU cc_start: 0.7785 (pp20) cc_final: 0.7481 (mm-30) REVERT: B 387 ILE cc_start: 0.8046 (mp) cc_final: 0.7680 (mt) REVERT: B 494 SER cc_start: 0.8785 (m) cc_final: 0.8303 (p) REVERT: B 613 GLU cc_start: 0.8182 (tt0) cc_final: 0.7973 (tt0) REVERT: B 773 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 776 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 876 GLN cc_start: 0.8682 (tp40) cc_final: 0.8192 (tm-30) REVERT: B 1075 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7544 (mp) REVERT: C 154 LYS cc_start: 0.8922 (tttm) cc_final: 0.8225 (mttp) REVERT: C 301 LYS cc_start: 0.8336 (tmmt) cc_final: 0.7678 (tptt) REVERT: C 305 LYS cc_start: 0.7940 (ptpt) cc_final: 0.7667 (tptt) REVERT: C 321 GLU cc_start: 0.8497 (pm20) cc_final: 0.8111 (pm20) REVERT: C 364 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5517 (pm20) REVERT: C 387 ILE cc_start: 0.8016 (mp) cc_final: 0.7639 (mt) REVERT: C 494 SER cc_start: 0.8815 (m) cc_final: 0.8331 (p) REVERT: C 557 ILE cc_start: 0.9124 (mt) cc_final: 0.8845 (mt) REVERT: C 771 CYS cc_start: 0.8817 (t) cc_final: 0.8480 (t) REVERT: C 773 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8257 (mm-30) REVERT: C 876 GLN cc_start: 0.8611 (tp40) cc_final: 0.8276 (tm-30) REVERT: C 1075 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7578 (mp) REVERT: D 154 LYS cc_start: 0.8949 (tttm) cc_final: 0.8335 (mttp) REVERT: D 387 ILE cc_start: 0.8045 (mp) cc_final: 0.7622 (mt) REVERT: D 494 SER cc_start: 0.8848 (m) cc_final: 0.8358 (p) REVERT: D 685 LYS cc_start: 0.8807 (tttt) cc_final: 0.8605 (ttmt) REVERT: D 771 CYS cc_start: 0.8708 (t) cc_final: 0.8480 (t) REVERT: D 776 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 784 TYR cc_start: 0.7698 (t80) cc_final: 0.7259 (t80) REVERT: D 790 ASN cc_start: 0.8210 (t0) cc_final: 0.7925 (t0) REVERT: D 876 GLN cc_start: 0.8609 (tp40) cc_final: 0.8068 (tm-30) REVERT: D 1075 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7401 (mp) outliers start: 62 outliers final: 51 residues processed: 574 average time/residue: 0.1750 time to fit residues: 164.1201 Evaluate side-chains 567 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 511 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 428 ASN Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 777 TRP Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 700 PHE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 44 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 328 optimal weight: 0.0070 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 126 GLN C 550 HIS D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.183998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140809 restraints weight = 33408.731| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.53 r_work: 0.3252 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28384 Z= 0.117 Angle : 0.597 12.527 38324 Z= 0.302 Chirality : 0.042 0.206 4268 Planarity : 0.004 0.050 4684 Dihedral : 7.227 61.467 3820 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.12 % Allowed : 21.70 % Favored : 76.18 % 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: -0.98 (0.15), residues: 3252 helix: 0.40 (0.11), residues: 2196 sheet: -2.43 (0.45), residues: 140 loop : -2.91 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.056 0.001 TYR D 286 PHE 0.022 0.001 PHE D 858 TRP 0.041 0.001 TRP A 684 HIS 0.004 0.000 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (28376) covalent geometry : angle 0.59679 / 0.30 (38324) hydrogen bonds : bond 0.03090 / 2.07 ( 1260) hydrogen bonds : angle 3.66163 / 2.54 ( 3744) Misc. bond : bond 0.00033 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7025.90 seconds wall clock time: 121 minutes 14.81 seconds (7274.81 seconds total)