Starting phenix.real_space_refine on Fri Mar 6 06:50:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o77_0639/03_2026/6o77_0639.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o77_0639/03_2026/6o77_0639.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6o77_0639/03_2026/6o77_0639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o77_0639/03_2026/6o77_0639.map" model { file = "/net/cci-nas-00/data/ceres_data/6o77_0639/03_2026/6o77_0639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o77_0639/03_2026/6o77_0639.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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 18884 2.51 5 N 4688 2.21 5 O 5168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28884 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7115 Classifications: {'peptide': 872} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 849} Chain breaks: 11 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 7.26, per 1000 atoms: 0.25 Number of scatterers: 28884 At special positions: 0 Unit cell: (126.021, 126.021, 153.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5168 8.00 N 4688 7.00 C 18884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A 930 " distance=2.03 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 930 " distance=2.03 Simple disulfide: pdb=" SG CYS C 919 " - pdb=" SG CYS C 930 " distance=2.03 Simple disulfide: pdb=" SG CYS D 919 " - pdb=" SG CYS D 930 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 65.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.691A pdb=" N LYS A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 348 " --> pdb=" O CYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (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 406 removed outlier: 3.995A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.735A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.555A pdb=" N THR A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 459 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS A 517 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA A 554 " --> pdb=" O HIS A 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.639A pdb=" N ALA A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.801A pdb=" N ALA A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (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 682 through 689 removed outlier: 3.921A pdb=" N ILE A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR A 723 " --> pdb=" O SER A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE A 735 " --> pdb=" O TRP A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 removed outlier: 4.366A pdb=" N LYS A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 959 removed outlier: 3.630A pdb=" N ASN A 958 " --> pdb=" O MET A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 976 removed outlier: 3.582A pdb=" N ALA A 967 " --> pdb=" O ASN A 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 972 " --> pdb=" O MET A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 removed outlier: 4.208A pdb=" N GLN A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1041 through 1061 removed outlier: 3.858A pdb=" N ALA A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP A1076 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1077 " --> pdb=" O ARG A1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A1078 " --> pdb=" O GLN A1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.580A pdb=" N HIS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 3.603A pdb=" N PHE B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 removed outlier: 3.690A pdb=" N LYS B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 348 " --> pdb=" O CYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 376 removed outlier: 3.845A pdb=" N GLU B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (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 406 removed outlier: 3.995A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.736A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.621A pdb=" N ALA B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS B 517 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.641A pdb=" N ALA B 554 " --> pdb=" O HIS B 550 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 removed outlier: 3.640A pdb=" N ALA B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.801A pdb=" N ALA B 651 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (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 682 through 689 removed outlier: 3.920A pdb=" N ILE B 686 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR B 723 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE B 735 " --> pdb=" O TRP B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 793 " --> pdb=" O TRP B 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 851 removed outlier: 4.367A pdb=" N LYS B 846 " --> pdb=" O ASN B 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 848 " --> pdb=" O GLY B 844 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 900 removed outlier: 3.562A pdb=" N ALA B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN B 958 " --> pdb=" O MET B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 976 removed outlier: 3.583A pdb=" N ALA B 967 " --> pdb=" O ASN B 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 972 " --> pdb=" O MET B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 994 removed outlier: 4.208A pdb=" N GLN B 982 " --> pdb=" O GLU B 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 989 " --> pdb=" O LYS B 985 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'B' and resid 1041 through 1061 removed outlier: 3.858A pdb=" N ALA B1061 " --> pdb=" O ILE B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP B1076 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B1077 " --> pdb=" O ARG B1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS B1078 " --> pdb=" O GLN B1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B1080 " --> pdb=" O ASP B1076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP B1081 " --> pdb=" O ALA B1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.690A pdb=" N LYS C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 348 " --> pdb=" O CYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (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 406 removed outlier: 3.995A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.736A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 459 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS C 517 " --> pdb=" O THR C 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 518 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 595 removed outlier: 3.638A pdb=" N ALA C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.800A pdb=" N ALA C 651 " --> pdb=" O CYS C 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (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 682 through 689 removed outlier: 3.920A pdb=" N ILE C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR C 723 " --> pdb=" O SER C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE C 735 " --> pdb=" O TRP C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE C 760 " --> pdb=" O THR C 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 787 Processing helix chain 'C' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 831 removed outlier: 3.607A pdb=" N TYR C 816 " --> pdb=" O GLU C 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 removed outlier: 4.367A pdb=" N LYS C 846 " --> pdb=" O ASN C 842 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 848 " --> pdb=" O GLY C 844 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 851 " --> pdb=" O ILE C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 875 removed outlier: 3.534A pdb=" N ALA C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN C 958 " --> pdb=" O MET C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 976 removed outlier: 3.582A pdb=" N ALA C 967 " --> pdb=" O ASN C 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 994 removed outlier: 4.209A pdb=" N GLN C 982 " --> pdb=" O GLU C 978 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 989 " --> pdb=" O LYS C 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'C' and resid 1041 through 1061 removed outlier: 3.857A pdb=" N ALA C1061 " --> pdb=" O ILE C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP C1076 " --> pdb=" O PHE C1072 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C1077 " --> pdb=" O ARG C1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS C1078 " --> pdb=" O GLN C1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C1080 " --> pdb=" O ASP C1076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C1081 " --> pdb=" O ALA C1077 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 267 through 279 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.708A pdb=" N SER D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.691A pdb=" N LYS D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 348 " --> pdb=" O CYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (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 406 removed outlier: 3.995A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.735A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA D 433 " --> pdb=" O GLN D 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 459 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.969A pdb=" N LYS D 517 " --> pdb=" O THR D 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D 518 " --> pdb=" O PHE D 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.638A pdb=" N ALA D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.800A pdb=" N ALA D 651 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (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 682 through 689 removed outlier: 3.920A pdb=" N ILE D 686 " --> pdb=" O LYS D 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR D 723 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE D 735 " --> pdb=" O TRP D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 787 Processing helix chain 'D' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 793 " --> pdb=" O TRP D 789 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 837 removed outlier: 4.157A pdb=" N HIS D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 851 removed outlier: 4.366A pdb=" N LYS D 846 " --> pdb=" O ASN D 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 848 " --> pdb=" O GLY D 844 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 851 " --> pdb=" O ILE D 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA D 874 " --> pdb=" O ALA D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 887 Processing helix chain 'D' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA D 900 " --> pdb=" O GLU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN D 958 " --> pdb=" O MET D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 976 removed outlier: 3.583A pdb=" N ALA D 967 " --> pdb=" O ASN D 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 972 " --> pdb=" O MET D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 994 removed outlier: 4.209A pdb=" N GLN D 982 " --> pdb=" O GLU D 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE D 989 " --> pdb=" O LYS D 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1041 through 1061 removed outlier: 3.857A pdb=" N ALA D1061 " --> pdb=" O ILE D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP D1076 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D1077 " --> pdb=" O ARG D1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS D1078 " --> pdb=" O GLN D1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1079 " --> pdb=" O LEU D1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D1080 " --> pdb=" O ASP D1076 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.792A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU A 253 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 109 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.792A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 253 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 109 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.791A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU C 253 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE C 109 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.793A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU D 253 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE D 109 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3984 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: 5.09 Time building geometry restraints manager: 3.26 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: 4644 1.31 - 1.43: 8156 1.43 - 1.56: 16412 1.56 - 1.69: 88 1.69 - 1.82: 252 Bond restraints: 29552 Sorted by residual: bond pdb=" CAI Y01 C1403 " pdb=" CAZ Y01 C1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 D1403 " pdb=" CAZ Y01 D1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 A1403 " pdb=" CAZ Y01 A1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 B1403 " pdb=" CAZ Y01 B1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 D1402 " pdb=" CAZ Y01 D1402 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 ... (remaining 29547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 39359 3.34 - 6.67: 574 6.67 - 10.01: 87 10.01 - 13.34: 4 13.34 - 16.68: 8 Bond angle restraints: 40032 Sorted by residual: angle pdb=" C ASP D 907 " pdb=" N ASP D 908 " pdb=" CA ASP D 908 " ideal model delta sigma weight residual 121.83 112.81 9.02 1.48e+00 4.57e-01 3.71e+01 angle pdb=" C ASP A 907 " pdb=" N ASP A 908 " pdb=" CA ASP A 908 " ideal model delta sigma weight residual 121.83 112.82 9.01 1.48e+00 4.57e-01 3.70e+01 angle pdb=" C ASP C 907 " pdb=" N ASP C 908 " pdb=" CA ASP C 908 " ideal model delta sigma weight residual 121.83 112.82 9.01 1.48e+00 4.57e-01 3.70e+01 angle pdb=" C ASP B 907 " pdb=" N ASP B 908 " pdb=" CA ASP B 908 " ideal model delta sigma weight residual 121.83 112.83 9.00 1.48e+00 4.57e-01 3.70e+01 angle pdb=" N ASP A 907 " pdb=" CA ASP A 907 " pdb=" C ASP A 907 " ideal model delta sigma weight residual 111.33 118.07 -6.74 1.21e+00 6.83e-01 3.10e+01 ... (remaining 40027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15905 17.97 - 35.94: 1747 35.94 - 53.91: 264 53.91 - 71.88: 64 71.88 - 89.85: 28 Dihedral angle restraints: 18008 sinusoidal: 7804 harmonic: 10204 Sorted by residual: dihedral pdb=" CA GLN C 876 " pdb=" C GLN C 876 " pdb=" N GLY C 877 " pdb=" CA GLY C 877 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN D 876 " pdb=" C GLN D 876 " pdb=" N GLY D 877 " pdb=" CA GLY D 877 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN B 876 " pdb=" C GLN B 876 " pdb=" N GLY B 877 " pdb=" CA GLY B 877 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 18005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4285 0.114 - 0.228: 155 0.228 - 0.342: 24 0.342 - 0.456: 8 0.456 - 0.571: 12 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CBI Y01 B1404 " pdb=" CAU Y01 B1404 " pdb=" CBE Y01 B1404 " pdb=" CBG Y01 B1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CBI Y01 D1404 " pdb=" CAU Y01 D1404 " pdb=" CBE Y01 D1404 " pdb=" CBG Y01 D1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CBI Y01 A1404 " pdb=" CAU Y01 A1404 " pdb=" CBE Y01 A1404 " pdb=" CBG Y01 A1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.08e+00 ... (remaining 4481 not shown) Planarity restraints: 4928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 905 " 0.108 5.00e-02 4.00e+02 1.64e-01 4.33e+01 pdb=" N PRO B 906 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 906 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 906 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 905 " -0.108 5.00e-02 4.00e+02 1.64e-01 4.33e+01 pdb=" N PRO C 906 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 906 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 906 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 905 " -0.108 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO D 906 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO D 906 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO D 906 " -0.080 5.00e-02 4.00e+02 ... (remaining 4925 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 20 2.26 - 2.92: 11749 2.92 - 3.58: 40812 3.58 - 4.24: 69088 4.24 - 4.90: 113633 Nonbonded interactions: 235302 Sorted by model distance: nonbonded pdb=" CH2 TRP A 888 " pdb=" O SER A 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP D 888 " pdb=" O SER D 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP B 888 " pdb=" O SER B 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP C 888 " pdb=" O SER C 926 " model vdw 1.604 3.340 nonbonded pdb=" CZ3 TRP D 888 " pdb=" O SER D 926 " model vdw 2.016 3.340 ... (remaining 235297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.380 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.364 29556 Z= 0.609 Angle : 1.006 16.675 40040 Z= 0.517 Chirality : 0.063 0.571 4484 Planarity : 0.007 0.164 4928 Dihedral : 15.188 89.851 11364 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -5.77 (0.10), residues: 3392 helix: -4.01 (0.05), residues: 2156 sheet: -2.45 (0.33), residues: 208 loop : -3.09 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 655 TYR 0.016 0.002 TYR C 971 PHE 0.021 0.002 PHE B 806 TRP 0.023 0.003 TRP D 516 HIS 0.009 0.002 HIS D 129 Details of bonding type rmsd covalent geometry : bond 0.01251 (29552) covalent geometry : angle 1.00618 (40032) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.70704 ( 8) hydrogen bonds : bond 0.27470 ( 1340) hydrogen bonds : angle 9.61019 ( 3984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 953 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8035 (ttt180) cc_final: 0.6296 (ptp-170) REVERT: A 149 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8587 (mtmt) REVERT: A 323 SER cc_start: 0.8416 (m) cc_final: 0.7928 (m) REVERT: A 592 MET cc_start: 0.8462 (mmm) cc_final: 0.8173 (mmp) REVERT: A 606 GLU cc_start: 0.8298 (pp20) cc_final: 0.7845 (pp20) REVERT: A 611 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 649 GLU cc_start: 0.8034 (mp0) cc_final: 0.7663 (pm20) REVERT: A 672 GLN cc_start: 0.8006 (tt0) cc_final: 0.7768 (tt0) REVERT: A 674 TYR cc_start: 0.8270 (m-80) cc_final: 0.7896 (m-10) REVERT: A 688 MET cc_start: 0.7379 (mtp) cc_final: 0.6331 (ppp) REVERT: A 775 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7544 (ttt180) REVERT: A 789 TRP cc_start: 0.8714 (m100) cc_final: 0.8308 (m100) REVERT: A 790 ASN cc_start: 0.9162 (m-40) cc_final: 0.8789 (t0) REVERT: A 798 PHE cc_start: 0.8640 (t80) cc_final: 0.8414 (t80) REVERT: A 825 ASP cc_start: 0.8431 (t0) cc_final: 0.8190 (t0) REVERT: A 841 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6726 (ttp80) REVERT: A 887 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 955 LEU cc_start: 0.9183 (tp) cc_final: 0.8925 (tp) REVERT: A 1056 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8762 (ttpp) REVERT: B 110 ARG cc_start: 0.8070 (ttt180) cc_final: 0.6282 (ptp-170) REVERT: B 149 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8571 (mtmt) REVERT: B 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8173 (mmp) REVERT: B 606 GLU cc_start: 0.8296 (pp20) cc_final: 0.7853 (pp20) REVERT: B 649 GLU cc_start: 0.8049 (mp0) cc_final: 0.7666 (pm20) REVERT: B 672 GLN cc_start: 0.8008 (tt0) cc_final: 0.7772 (tt0) REVERT: B 674 TYR cc_start: 0.8269 (m-80) cc_final: 0.7901 (m-10) REVERT: B 688 MET cc_start: 0.7370 (mtp) cc_final: 0.6334 (ppp) REVERT: B 775 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7573 (ttt180) REVERT: B 789 TRP cc_start: 0.8719 (m100) cc_final: 0.8313 (m100) REVERT: B 790 ASN cc_start: 0.9163 (m-40) cc_final: 0.8792 (t0) REVERT: B 798 PHE cc_start: 0.8638 (t80) cc_final: 0.8390 (t80) REVERT: B 825 ASP cc_start: 0.8401 (t0) cc_final: 0.8152 (t0) REVERT: B 841 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6744 (ttp80) REVERT: B 887 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 955 LEU cc_start: 0.9186 (tp) cc_final: 0.8940 (tp) REVERT: C 110 ARG cc_start: 0.8071 (ttt180) cc_final: 0.6281 (ptp-170) REVERT: C 149 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8571 (mtmt) REVERT: C 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8174 (mmp) REVERT: C 606 GLU cc_start: 0.8299 (pp20) cc_final: 0.7856 (pp20) REVERT: C 649 GLU cc_start: 0.8046 (mp0) cc_final: 0.7661 (pm20) REVERT: C 672 GLN cc_start: 0.8007 (tt0) cc_final: 0.7772 (tt0) REVERT: C 674 TYR cc_start: 0.8270 (m-80) cc_final: 0.7899 (m-10) REVERT: C 688 MET cc_start: 0.7367 (mtp) cc_final: 0.6332 (ppp) REVERT: C 775 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7566 (ttt180) REVERT: C 789 TRP cc_start: 0.8720 (m100) cc_final: 0.8324 (m100) REVERT: C 790 ASN cc_start: 0.9164 (m-40) cc_final: 0.8785 (t0) REVERT: C 798 PHE cc_start: 0.8636 (t80) cc_final: 0.8388 (t80) REVERT: C 825 ASP cc_start: 0.8398 (t0) cc_final: 0.8147 (t0) REVERT: C 841 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6743 (ttp80) REVERT: C 887 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 955 LEU cc_start: 0.9184 (tp) cc_final: 0.8939 (tp) REVERT: D 110 ARG cc_start: 0.8069 (ttt180) cc_final: 0.6288 (ptp-170) REVERT: D 149 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8573 (mtmt) REVERT: D 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8173 (mmp) REVERT: D 606 GLU cc_start: 0.8298 (pp20) cc_final: 0.7858 (pp20) REVERT: D 649 GLU cc_start: 0.8048 (mp0) cc_final: 0.7664 (pm20) REVERT: D 672 GLN cc_start: 0.8007 (tt0) cc_final: 0.7773 (tt0) REVERT: D 674 TYR cc_start: 0.8267 (m-80) cc_final: 0.7896 (m-10) REVERT: D 688 MET cc_start: 0.7368 (mtp) cc_final: 0.6332 (ppp) REVERT: D 775 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7565 (ttt180) REVERT: D 789 TRP cc_start: 0.8719 (m100) cc_final: 0.8324 (m100) REVERT: D 790 ASN cc_start: 0.9163 (m-40) cc_final: 0.8789 (t0) REVERT: D 798 PHE cc_start: 0.8637 (t80) cc_final: 0.8389 (t80) REVERT: D 825 ASP cc_start: 0.8401 (t0) cc_final: 0.8148 (t0) REVERT: D 841 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6746 (ttp80) REVERT: D 887 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7392 (mt-10) REVERT: D 955 LEU cc_start: 0.9185 (tp) cc_final: 0.8937 (tp) outliers start: 0 outliers final: 0 residues processed: 953 average time/residue: 0.2018 time to fit residues: 296.1354 Evaluate side-chains 770 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 770 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 213 ASN A 248 HIS A 308 ASN A 380 HIS A 440 ASN A 662 GLN A 666 GLN A 683 ASN A 882 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 GLN B 145 ASN B 213 ASN B 248 HIS B 308 ASN B 380 HIS B 440 ASN B 662 GLN B 666 GLN B 683 ASN B 882 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 GLN C 145 ASN C 213 ASN C 248 HIS C 308 ASN C 440 ASN C 662 GLN C 666 GLN C 683 ASN C 882 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 GLN D 145 ASN D 213 ASN D 248 HIS D 380 HIS D 440 ASN D 662 GLN D 666 GLN D 683 ASN D 882 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125654 restraints weight = 44489.317| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.66 r_work: 0.3336 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29556 Z= 0.149 Angle : 0.672 12.166 40040 Z= 0.349 Chirality : 0.044 0.210 4484 Planarity : 0.006 0.149 4928 Dihedral : 7.635 53.573 4588 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.46 % Rotamer: Outliers : 1.51 % Allowed : 13.56 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.12), residues: 3392 helix: -1.90 (0.09), residues: 2208 sheet: -2.18 (0.35), residues: 196 loop : -2.92 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 875 TYR 0.019 0.001 TYR D 905 PHE 0.026 0.001 PHE D 921 TRP 0.017 0.001 TRP D 444 HIS 0.004 0.001 HIS D 129 Details of bonding type rmsd covalent geometry : bond 0.00344 (29552) covalent geometry : angle 0.67215 (40032) SS BOND : bond 0.00599 ( 4) SS BOND : angle 1.57641 ( 8) hydrogen bonds : bond 0.05262 ( 1340) hydrogen bonds : angle 4.82709 ( 3984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 811 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 SER cc_start: 0.8433 (m) cc_final: 0.8139 (m) REVERT: A 592 MET cc_start: 0.8510 (mmm) cc_final: 0.8185 (mmp) REVERT: A 611 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 649 GLU cc_start: 0.8531 (mp0) cc_final: 0.8154 (pm20) REVERT: A 672 GLN cc_start: 0.8199 (tt0) cc_final: 0.7902 (tt0) REVERT: A 674 TYR cc_start: 0.8649 (m-80) cc_final: 0.8326 (m-80) REVERT: A 688 MET cc_start: 0.7701 (mtp) cc_final: 0.6511 (tmm) REVERT: A 789 TRP cc_start: 0.8623 (m100) cc_final: 0.8286 (m100) REVERT: A 790 ASN cc_start: 0.9268 (m-40) cc_final: 0.8876 (m-40) REVERT: A 798 PHE cc_start: 0.8903 (t80) cc_final: 0.8683 (t80) REVERT: A 832 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8675 (mtp85) REVERT: A 841 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7484 (ttp80) REVERT: B 592 MET cc_start: 0.8514 (mmm) cc_final: 0.8192 (mmp) REVERT: B 611 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 649 GLU cc_start: 0.8527 (mp0) cc_final: 0.8140 (pm20) REVERT: B 672 GLN cc_start: 0.8195 (tt0) cc_final: 0.7899 (tt0) REVERT: B 674 TYR cc_start: 0.8666 (m-80) cc_final: 0.8344 (m-80) REVERT: B 688 MET cc_start: 0.7729 (mtp) cc_final: 0.6549 (tmm) REVERT: B 789 TRP cc_start: 0.8620 (m100) cc_final: 0.8280 (m100) REVERT: B 790 ASN cc_start: 0.9275 (m-40) cc_final: 0.8853 (m-40) REVERT: B 798 PHE cc_start: 0.8886 (t80) cc_final: 0.8670 (t80) REVERT: B 841 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7444 (ttp80) REVERT: B 955 LEU cc_start: 0.9312 (tp) cc_final: 0.8985 (tp) REVERT: C 592 MET cc_start: 0.8522 (mmm) cc_final: 0.8199 (mmp) REVERT: C 607 GLU cc_start: 0.8802 (tp30) cc_final: 0.8239 (tp30) REVERT: C 649 GLU cc_start: 0.8542 (mp0) cc_final: 0.8143 (pm20) REVERT: C 672 GLN cc_start: 0.8231 (tt0) cc_final: 0.7941 (tt0) REVERT: C 674 TYR cc_start: 0.8653 (m-80) cc_final: 0.8331 (m-80) REVERT: C 688 MET cc_start: 0.7737 (mtp) cc_final: 0.6551 (tmm) REVERT: C 789 TRP cc_start: 0.8632 (m100) cc_final: 0.8296 (m100) REVERT: C 790 ASN cc_start: 0.9265 (m-40) cc_final: 0.8872 (m-40) REVERT: C 798 PHE cc_start: 0.8894 (t80) cc_final: 0.8676 (t80) REVERT: C 841 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7388 (ttp80) REVERT: C 955 LEU cc_start: 0.9310 (tp) cc_final: 0.8982 (tp) REVERT: C 1068 MET cc_start: 0.4389 (ttt) cc_final: 0.4126 (pmm) REVERT: D 592 MET cc_start: 0.8519 (mmm) cc_final: 0.8198 (mmp) REVERT: D 607 GLU cc_start: 0.8798 (tp30) cc_final: 0.8234 (tp30) REVERT: D 649 GLU cc_start: 0.8537 (mp0) cc_final: 0.8141 (pm20) REVERT: D 672 GLN cc_start: 0.8225 (tt0) cc_final: 0.7925 (tt0) REVERT: D 674 TYR cc_start: 0.8649 (m-80) cc_final: 0.8326 (m-80) REVERT: D 688 MET cc_start: 0.7733 (mtp) cc_final: 0.6547 (tmm) REVERT: D 789 TRP cc_start: 0.8627 (m100) cc_final: 0.8291 (m100) REVERT: D 790 ASN cc_start: 0.9268 (m-40) cc_final: 0.8870 (m-40) REVERT: D 798 PHE cc_start: 0.8899 (t80) cc_final: 0.8686 (t80) REVERT: D 841 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7442 (ttp80) REVERT: D 955 LEU cc_start: 0.9313 (tp) cc_final: 0.8988 (tp) outliers start: 47 outliers final: 26 residues processed: 823 average time/residue: 0.1835 time to fit residues: 240.0398 Evaluate side-chains 744 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 718 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 888 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 188 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 197 optimal weight: 0.0970 chunk 328 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 183 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126034 restraints weight = 44369.808| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.88 r_work: 0.3324 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29556 Z= 0.124 Angle : 0.595 11.482 40040 Z= 0.307 Chirality : 0.042 0.188 4484 Planarity : 0.005 0.139 4928 Dihedral : 6.879 50.446 4588 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.98 % Favored : 93.90 % Rotamer: Outliers : 2.09 % Allowed : 15.55 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -2.22 (0.13), residues: 3392 helix: -0.73 (0.10), residues: 2220 sheet: -2.01 (0.36), residues: 196 loop : -2.87 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 875 TYR 0.015 0.001 TYR D 905 PHE 0.024 0.001 PHE B 921 TRP 0.016 0.001 TRP A 444 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00291 (29552) covalent geometry : angle 0.59451 (40032) SS BOND : bond 0.00659 ( 4) SS BOND : angle 1.96316 ( 8) hydrogen bonds : bond 0.03875 ( 1340) hydrogen bonds : angle 4.22354 ( 3984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 837 time to evaluate : 1.081 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 323 SER cc_start: 0.8276 (m) cc_final: 0.7933 (m) REVERT: A 592 MET cc_start: 0.8411 (mmm) cc_final: 0.8014 (mmp) REVERT: A 611 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 628 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8381 (mt-10) REVERT: A 637 TYR cc_start: 0.7821 (m-10) cc_final: 0.7556 (t80) REVERT: A 645 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.6536 (t) REVERT: A 649 GLU cc_start: 0.8752 (mp0) cc_final: 0.8076 (mp0) REVERT: A 674 TYR cc_start: 0.8678 (m-80) cc_final: 0.8321 (m-80) REVERT: A 688 MET cc_start: 0.7753 (mtp) cc_final: 0.6390 (tmm) REVERT: A 785 PHE cc_start: 0.8540 (m-10) cc_final: 0.8146 (m-10) REVERT: A 798 PHE cc_start: 0.8759 (t80) cc_final: 0.8509 (t80) REVERT: A 841 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7507 (ttp80) REVERT: A 904 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 955 LEU cc_start: 0.9314 (tp) cc_final: 0.8996 (tp) REVERT: B 323 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8022 (m) REVERT: B 592 MET cc_start: 0.8397 (mmm) cc_final: 0.8016 (mmp) REVERT: B 607 GLU cc_start: 0.8884 (tp30) cc_final: 0.8279 (tp30) REVERT: B 637 TYR cc_start: 0.7809 (m-10) cc_final: 0.7564 (t80) REVERT: B 645 SER cc_start: 0.7515 (OUTLIER) cc_final: 0.6418 (t) REVERT: B 649 GLU cc_start: 0.8753 (mp0) cc_final: 0.8074 (mp0) REVERT: B 674 TYR cc_start: 0.8679 (m-80) cc_final: 0.8318 (m-80) REVERT: B 688 MET cc_start: 0.7593 (mtp) cc_final: 0.6370 (tmm) REVERT: B 785 PHE cc_start: 0.8510 (m-10) cc_final: 0.8120 (m-10) REVERT: B 789 TRP cc_start: 0.8763 (m100) cc_final: 0.8327 (m100) REVERT: B 841 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7496 (ttp80) REVERT: B 898 TYR cc_start: 0.9359 (t80) cc_final: 0.8710 (t80) REVERT: B 904 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8566 (tm-30) REVERT: B 955 LEU cc_start: 0.9315 (tp) cc_final: 0.9010 (tp) REVERT: C 323 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8024 (m) REVERT: C 592 MET cc_start: 0.8403 (mmm) cc_final: 0.8020 (mmp) REVERT: C 607 GLU cc_start: 0.8883 (tp30) cc_final: 0.8275 (tp30) REVERT: C 637 TYR cc_start: 0.7755 (m-10) cc_final: 0.7529 (t80) REVERT: C 645 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.6420 (t) REVERT: C 649 GLU cc_start: 0.8745 (mp0) cc_final: 0.8070 (mp0) REVERT: C 674 TYR cc_start: 0.8675 (m-80) cc_final: 0.8309 (m-80) REVERT: C 688 MET cc_start: 0.7620 (mtp) cc_final: 0.6347 (tmm) REVERT: C 785 PHE cc_start: 0.8540 (m-10) cc_final: 0.8150 (m-10) REVERT: C 789 TRP cc_start: 0.8780 (m100) cc_final: 0.8328 (m100) REVERT: C 841 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7431 (ttp80) REVERT: C 898 TYR cc_start: 0.9358 (t80) cc_final: 0.8708 (t80) REVERT: C 904 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8575 (tm-30) REVERT: C 955 LEU cc_start: 0.9313 (tp) cc_final: 0.9011 (tp) REVERT: C 1068 MET cc_start: 0.4429 (ttt) cc_final: 0.3725 (pmm) REVERT: D 323 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8014 (m) REVERT: D 592 MET cc_start: 0.8401 (mmm) cc_final: 0.8017 (mmp) REVERT: D 607 GLU cc_start: 0.8887 (tp30) cc_final: 0.8280 (tp30) REVERT: D 637 TYR cc_start: 0.7742 (m-10) cc_final: 0.7528 (t80) REVERT: D 645 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.6446 (t) REVERT: D 649 GLU cc_start: 0.8751 (mp0) cc_final: 0.8072 (mp0) REVERT: D 674 TYR cc_start: 0.8679 (m-80) cc_final: 0.8313 (m-80) REVERT: D 688 MET cc_start: 0.7606 (mtp) cc_final: 0.6378 (tmm) REVERT: D 785 PHE cc_start: 0.8538 (m-10) cc_final: 0.8149 (m-10) REVERT: D 841 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7486 (ttp80) REVERT: D 898 TYR cc_start: 0.9363 (t80) cc_final: 0.8628 (t80) REVERT: D 953 TYR cc_start: 0.9515 (t80) cc_final: 0.9118 (t80) REVERT: D 955 LEU cc_start: 0.9315 (tp) cc_final: 0.9007 (tp) REVERT: D 1068 MET cc_start: 0.4966 (ttt) cc_final: 0.4378 (ptm) outliers start: 65 outliers final: 24 residues processed: 865 average time/residue: 0.1727 time to fit residues: 242.4040 Evaluate side-chains 768 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 737 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 905 TYR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 905 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 232 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 222 optimal weight: 0.2980 chunk 253 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125748 restraints weight = 44251.407| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.86 r_work: 0.3317 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29556 Z= 0.131 Angle : 0.583 11.143 40040 Z= 0.302 Chirality : 0.042 0.193 4484 Planarity : 0.005 0.132 4928 Dihedral : 6.582 50.894 4588 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.28 % Rotamer: Outliers : 2.67 % Allowed : 17.71 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.60 (0.14), residues: 3392 helix: -0.17 (0.11), residues: 2204 sheet: -1.95 (0.36), residues: 196 loop : -2.77 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 875 TYR 0.012 0.001 TYR C 905 PHE 0.015 0.001 PHE A 921 TRP 0.030 0.001 TRP C 516 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00314 (29552) covalent geometry : angle 0.58282 (40032) SS BOND : bond 0.00704 ( 4) SS BOND : angle 1.81800 ( 8) hydrogen bonds : bond 0.03581 ( 1340) hydrogen bonds : angle 4.08206 ( 3984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 761 time to evaluate : 1.073 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 306 SER cc_start: 0.9149 (t) cc_final: 0.8573 (p) REVERT: A 323 SER cc_start: 0.8303 (m) cc_final: 0.8041 (m) REVERT: A 592 MET cc_start: 0.8370 (mmm) cc_final: 0.8116 (mmp) REVERT: A 607 GLU cc_start: 0.8867 (tp30) cc_final: 0.8625 (tp30) REVERT: A 628 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8400 (mt-10) REVERT: A 645 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.6410 (t) REVERT: A 649 GLU cc_start: 0.8767 (mp0) cc_final: 0.8052 (mp0) REVERT: A 674 TYR cc_start: 0.8671 (m-80) cc_final: 0.8352 (m-80) REVERT: A 688 MET cc_start: 0.7627 (mtp) cc_final: 0.6400 (tmm) REVERT: A 789 TRP cc_start: 0.8750 (m100) cc_final: 0.8313 (m100) REVERT: A 790 ASN cc_start: 0.9125 (m-40) cc_final: 0.8604 (t0) REVERT: A 798 PHE cc_start: 0.8717 (t80) cc_final: 0.8461 (t80) REVERT: A 841 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 871 PHE cc_start: 0.9246 (t80) cc_final: 0.9040 (t80) REVERT: B 592 MET cc_start: 0.8359 (mmm) cc_final: 0.7910 (mmp) REVERT: B 606 GLU cc_start: 0.8536 (pp20) cc_final: 0.8119 (pp20) REVERT: B 607 GLU cc_start: 0.8893 (tp30) cc_final: 0.8365 (tp30) REVERT: B 628 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 645 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.6396 (t) REVERT: B 649 GLU cc_start: 0.8768 (mp0) cc_final: 0.8055 (mp0) REVERT: B 674 TYR cc_start: 0.8670 (m-80) cc_final: 0.8353 (m-80) REVERT: B 688 MET cc_start: 0.7613 (mtp) cc_final: 0.6397 (tmm) REVERT: B 789 TRP cc_start: 0.8763 (m100) cc_final: 0.8393 (m100) REVERT: B 808 LEU cc_start: 0.8449 (mt) cc_final: 0.8212 (mt) REVERT: B 841 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7480 (ttp80) REVERT: B 1068 MET cc_start: 0.4594 (pmm) cc_final: 0.3829 (mtt) REVERT: C 592 MET cc_start: 0.8360 (mmm) cc_final: 0.7913 (mmp) REVERT: C 606 GLU cc_start: 0.8536 (pp20) cc_final: 0.8119 (pp20) REVERT: C 607 GLU cc_start: 0.8877 (tp30) cc_final: 0.8349 (tp30) REVERT: C 628 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8429 (mt-10) REVERT: C 645 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.6403 (t) REVERT: C 649 GLU cc_start: 0.8762 (mp0) cc_final: 0.8050 (mp0) REVERT: C 674 TYR cc_start: 0.8668 (m-80) cc_final: 0.8350 (m-80) REVERT: C 688 MET cc_start: 0.7584 (mtp) cc_final: 0.6366 (tmm) REVERT: C 789 TRP cc_start: 0.8735 (m100) cc_final: 0.8349 (m100) REVERT: C 790 ASN cc_start: 0.9087 (m-40) cc_final: 0.8596 (t0) REVERT: C 808 LEU cc_start: 0.8471 (mt) cc_final: 0.8240 (mt) REVERT: C 841 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7548 (ttp80) REVERT: C 1068 MET cc_start: 0.4376 (ttt) cc_final: 0.3383 (pmm) REVERT: D 592 MET cc_start: 0.8370 (mmm) cc_final: 0.7924 (mmp) REVERT: D 606 GLU cc_start: 0.8541 (pp20) cc_final: 0.8122 (pp20) REVERT: D 607 GLU cc_start: 0.8882 (tp30) cc_final: 0.8354 (tp30) REVERT: D 628 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8429 (mt-10) REVERT: D 645 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.6411 (t) REVERT: D 649 GLU cc_start: 0.8770 (mp0) cc_final: 0.8052 (mp0) REVERT: D 674 TYR cc_start: 0.8667 (m-80) cc_final: 0.8346 (m-80) REVERT: D 688 MET cc_start: 0.7615 (mtp) cc_final: 0.6402 (tmm) REVERT: D 789 TRP cc_start: 0.8765 (m100) cc_final: 0.8347 (m100) REVERT: D 790 ASN cc_start: 0.9098 (m-40) cc_final: 0.8602 (t0) REVERT: D 808 LEU cc_start: 0.8445 (mt) cc_final: 0.8208 (mt) REVERT: D 841 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7514 (ttp80) outliers start: 83 outliers final: 39 residues processed: 796 average time/residue: 0.1759 time to fit residues: 226.7280 Evaluate side-chains 760 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 717 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 54 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 214 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 732 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 732 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.154991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124005 restraints weight = 44230.223| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.88 r_work: 0.3287 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29556 Z= 0.168 Angle : 0.604 10.734 40040 Z= 0.312 Chirality : 0.043 0.187 4484 Planarity : 0.005 0.124 4928 Dihedral : 6.469 51.119 4588 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 3.47 % Allowed : 18.35 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.31 (0.14), residues: 3392 helix: 0.06 (0.11), residues: 2224 sheet: -2.00 (0.35), residues: 196 loop : -2.70 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 359 TYR 0.014 0.001 TYR A 905 PHE 0.015 0.001 PHE D 921 TRP 0.040 0.002 TRP C 516 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00402 (29552) covalent geometry : angle 0.60239 (40032) SS BOND : bond 0.00498 ( 4) SS BOND : angle 2.71520 ( 8) hydrogen bonds : bond 0.03591 ( 1340) hydrogen bonds : angle 4.00784 ( 3984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 757 time to evaluate : 1.044 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 323 SER cc_start: 0.8461 (m) cc_final: 0.8212 (m) REVERT: A 486 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 628 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8445 (mt-10) REVERT: A 645 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.6355 (t) REVERT: A 649 GLU cc_start: 0.8809 (mp0) cc_final: 0.8012 (mp0) REVERT: A 674 TYR cc_start: 0.8698 (m-80) cc_final: 0.8327 (m-80) REVERT: A 688 MET cc_start: 0.7639 (mtp) cc_final: 0.6365 (tmm) REVERT: A 790 ASN cc_start: 0.9072 (m-40) cc_final: 0.8550 (t0) REVERT: A 798 PHE cc_start: 0.8715 (t80) cc_final: 0.8437 (t80) REVERT: A 841 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7599 (ttp80) REVERT: A 955 LEU cc_start: 0.9300 (tp) cc_final: 0.9047 (tp) REVERT: B 323 SER cc_start: 0.8616 (m) cc_final: 0.8398 (m) REVERT: B 486 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 553 GLN cc_start: 0.7625 (mp10) cc_final: 0.6797 (mp10) REVERT: B 606 GLU cc_start: 0.8513 (pp20) cc_final: 0.8092 (pp20) REVERT: B 607 GLU cc_start: 0.8910 (tp30) cc_final: 0.8400 (tp30) REVERT: B 628 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8462 (mt-10) REVERT: B 645 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.6340 (t) REVERT: B 649 GLU cc_start: 0.8806 (mp0) cc_final: 0.8024 (mp0) REVERT: B 674 TYR cc_start: 0.8700 (m-80) cc_final: 0.8327 (m-80) REVERT: B 688 MET cc_start: 0.7637 (mtp) cc_final: 0.6373 (tmm) REVERT: B 789 TRP cc_start: 0.8778 (m100) cc_final: 0.8475 (m100) REVERT: B 798 PHE cc_start: 0.8700 (t80) cc_final: 0.8428 (t80) REVERT: B 841 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7581 (ttp80) REVERT: B 955 LEU cc_start: 0.9302 (tp) cc_final: 0.9044 (tp) REVERT: C 323 SER cc_start: 0.8621 (m) cc_final: 0.8406 (m) REVERT: C 486 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8069 (mm-30) REVERT: C 606 GLU cc_start: 0.8526 (pp20) cc_final: 0.8112 (pp20) REVERT: C 607 GLU cc_start: 0.8906 (tp30) cc_final: 0.8397 (tp30) REVERT: C 628 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8457 (mt-10) REVERT: C 645 SER cc_start: 0.7620 (OUTLIER) cc_final: 0.6366 (t) REVERT: C 649 GLU cc_start: 0.8824 (mp0) cc_final: 0.8037 (mp0) REVERT: C 674 TYR cc_start: 0.8694 (m-80) cc_final: 0.8319 (m-80) REVERT: C 688 MET cc_start: 0.7629 (mtp) cc_final: 0.6370 (tmm) REVERT: C 789 TRP cc_start: 0.8766 (m100) cc_final: 0.8460 (m100) REVERT: C 790 ASN cc_start: 0.9052 (m-40) cc_final: 0.8539 (t0) REVERT: C 798 PHE cc_start: 0.8713 (t80) cc_final: 0.8446 (t80) REVERT: C 841 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7563 (ttp80) REVERT: C 955 LEU cc_start: 0.9287 (tp) cc_final: 0.9025 (tp) REVERT: C 1068 MET cc_start: 0.4494 (ttt) cc_final: 0.4207 (mtm) REVERT: D 323 SER cc_start: 0.8636 (m) cc_final: 0.8419 (m) REVERT: D 486 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8084 (mm-30) REVERT: D 606 GLU cc_start: 0.8512 (pp20) cc_final: 0.8096 (pp20) REVERT: D 607 GLU cc_start: 0.8906 (tp30) cc_final: 0.8397 (tp30) REVERT: D 628 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8473 (mt-10) REVERT: D 645 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.6351 (t) REVERT: D 649 GLU cc_start: 0.8820 (mp0) cc_final: 0.8031 (mp0) REVERT: D 674 TYR cc_start: 0.8689 (m-80) cc_final: 0.8314 (m-80) REVERT: D 688 MET cc_start: 0.7641 (mtp) cc_final: 0.6379 (tmm) REVERT: D 798 PHE cc_start: 0.8703 (t80) cc_final: 0.8434 (t80) REVERT: D 841 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7616 (ttp80) REVERT: D 955 LEU cc_start: 0.9295 (tp) cc_final: 0.9058 (tp) REVERT: D 1068 MET cc_start: 0.4766 (ttt) cc_final: 0.3702 (mtt) outliers start: 108 outliers final: 78 residues processed: 803 average time/residue: 0.1740 time to fit residues: 226.1459 Evaluate side-chains 773 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 691 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 417 TRP Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 732 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 417 TRP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 896 GLU Chi-restraints excluded: chain C residue 905 TYR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 732 ASN Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 331 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 247 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 646 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 646 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 646 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125892 restraints weight = 43885.133| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.84 r_work: 0.3309 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29556 Z= 0.125 Angle : 0.584 10.053 40040 Z= 0.302 Chirality : 0.042 0.222 4484 Planarity : 0.005 0.118 4928 Dihedral : 6.329 51.129 4588 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.92 % Rotamer: Outliers : 2.57 % Allowed : 20.73 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.09 (0.15), residues: 3392 helix: 0.22 (0.11), residues: 2228 sheet: -1.91 (0.35), residues: 196 loop : -2.59 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 832 TYR 0.013 0.001 TYR A 905 PHE 0.019 0.001 PHE A 921 TRP 0.046 0.002 TRP C 516 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00294 (29552) covalent geometry : angle 0.58325 (40032) SS BOND : bond 0.00462 ( 4) SS BOND : angle 2.40553 ( 8) hydrogen bonds : bond 0.03421 ( 1340) hydrogen bonds : angle 3.96414 ( 3984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 747 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.8528 (pp20) cc_final: 0.8121 (pp20) REVERT: A 607 GLU cc_start: 0.8884 (tp30) cc_final: 0.8373 (tp30) REVERT: A 628 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 645 SER cc_start: 0.7475 (OUTLIER) cc_final: 0.6152 (t) REVERT: A 646 ASN cc_start: 0.7645 (m-40) cc_final: 0.7106 (m110) REVERT: A 649 GLU cc_start: 0.8805 (mp0) cc_final: 0.7965 (mp0) REVERT: A 674 TYR cc_start: 0.8672 (m-80) cc_final: 0.8346 (m-80) REVERT: A 688 MET cc_start: 0.7621 (mtp) cc_final: 0.6353 (tmm) REVERT: A 779 MET cc_start: 0.8167 (tpp) cc_final: 0.7521 (ttm) REVERT: A 790 ASN cc_start: 0.9076 (m-40) cc_final: 0.8472 (t0) REVERT: A 798 PHE cc_start: 0.8712 (t80) cc_final: 0.8434 (t80) REVERT: A 841 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7649 (ttp80) REVERT: A 955 LEU cc_start: 0.9330 (tp) cc_final: 0.9113 (tp) REVERT: B 553 GLN cc_start: 0.7515 (mp10) cc_final: 0.6812 (mm-40) REVERT: B 606 GLU cc_start: 0.8516 (pp20) cc_final: 0.8092 (pp20) REVERT: B 607 GLU cc_start: 0.8884 (tp30) cc_final: 0.8378 (tp30) REVERT: B 628 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 645 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.6125 (t) REVERT: B 646 ASN cc_start: 0.7627 (m-40) cc_final: 0.7091 (m110) REVERT: B 649 GLU cc_start: 0.8814 (mp0) cc_final: 0.7988 (mp0) REVERT: B 674 TYR cc_start: 0.8674 (m-80) cc_final: 0.8354 (m-80) REVERT: B 688 MET cc_start: 0.7623 (mtp) cc_final: 0.6362 (tmm) REVERT: B 779 MET cc_start: 0.8258 (tpp) cc_final: 0.7322 (ttm) REVERT: B 789 TRP cc_start: 0.8717 (m100) cc_final: 0.8358 (m100) REVERT: B 798 PHE cc_start: 0.8703 (t80) cc_final: 0.8430 (t80) REVERT: B 832 ARG cc_start: 0.9032 (tpp80) cc_final: 0.8645 (mtp85) REVERT: B 841 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7599 (ttp80) REVERT: B 854 MET cc_start: 0.7946 (mmp) cc_final: 0.7613 (ptt) REVERT: B 898 TYR cc_start: 0.9380 (t80) cc_final: 0.8690 (t80) REVERT: B 955 LEU cc_start: 0.9331 (tp) cc_final: 0.9111 (tp) REVERT: C 297 GLN cc_start: 0.8655 (pp30) cc_final: 0.8322 (pp30) REVERT: C 606 GLU cc_start: 0.8516 (pp20) cc_final: 0.8093 (pp20) REVERT: C 607 GLU cc_start: 0.8883 (tp30) cc_final: 0.8379 (tp30) REVERT: C 628 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 645 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.6169 (t) REVERT: C 646 ASN cc_start: 0.7636 (m-40) cc_final: 0.7106 (m110) REVERT: C 649 GLU cc_start: 0.8819 (mp0) cc_final: 0.8003 (mp0) REVERT: C 674 TYR cc_start: 0.8666 (m-80) cc_final: 0.8341 (m-80) REVERT: C 688 MET cc_start: 0.7613 (mtp) cc_final: 0.6356 (tmm) REVERT: C 779 MET cc_start: 0.8254 (tpp) cc_final: 0.7617 (ttm) REVERT: C 789 TRP cc_start: 0.8692 (m100) cc_final: 0.8388 (m100) REVERT: C 790 ASN cc_start: 0.9036 (m-40) cc_final: 0.8470 (t0) REVERT: C 798 PHE cc_start: 0.8700 (t80) cc_final: 0.8433 (t80) REVERT: C 841 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7654 (ttp80) REVERT: C 854 MET cc_start: 0.7954 (mmp) cc_final: 0.7609 (ptt) REVERT: C 887 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: C 898 TYR cc_start: 0.9379 (t80) cc_final: 0.8694 (t80) REVERT: C 955 LEU cc_start: 0.9330 (tp) cc_final: 0.9114 (tp) REVERT: C 1068 MET cc_start: 0.4282 (ttt) cc_final: 0.4054 (mtm) REVERT: D 152 MET cc_start: 0.9181 (mmp) cc_final: 0.8965 (mmp) REVERT: D 297 GLN cc_start: 0.8664 (pp30) cc_final: 0.8281 (pp30) REVERT: D 606 GLU cc_start: 0.8511 (pp20) cc_final: 0.8085 (pp20) REVERT: D 607 GLU cc_start: 0.8881 (tp30) cc_final: 0.8376 (tp30) REVERT: D 628 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8429 (mt-10) REVERT: D 645 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.6129 (t) REVERT: D 646 ASN cc_start: 0.7625 (m-40) cc_final: 0.7088 (m110) REVERT: D 649 GLU cc_start: 0.8807 (mp0) cc_final: 0.7984 (mp0) REVERT: D 674 TYR cc_start: 0.8670 (m-80) cc_final: 0.8342 (m-80) REVERT: D 688 MET cc_start: 0.7622 (mtp) cc_final: 0.6368 (tmm) REVERT: D 779 MET cc_start: 0.8253 (tpp) cc_final: 0.7611 (ttm) REVERT: D 790 ASN cc_start: 0.9050 (m-40) cc_final: 0.8516 (t0) REVERT: D 798 PHE cc_start: 0.8691 (t80) cc_final: 0.8414 (t80) REVERT: D 841 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7631 (ttp80) REVERT: D 854 MET cc_start: 0.7949 (mmp) cc_final: 0.7610 (ptt) REVERT: D 898 TYR cc_start: 0.9375 (t80) cc_final: 0.8605 (t80) REVERT: D 955 LEU cc_start: 0.9325 (tp) cc_final: 0.9095 (tp) REVERT: D 1068 MET cc_start: 0.4910 (ttt) cc_final: 0.3825 (mtt) outliers start: 80 outliers final: 56 residues processed: 781 average time/residue: 0.1735 time to fit residues: 220.0933 Evaluate side-chains 790 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 729 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 417 TRP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 896 GLU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 138 optimal weight: 4.9990 chunk 332 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 226 optimal weight: 0.0980 chunk 254 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 732 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 732 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126847 restraints weight = 43888.437| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.87 r_work: 0.3315 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29556 Z= 0.123 Angle : 0.580 10.845 40040 Z= 0.299 Chirality : 0.042 0.178 4484 Planarity : 0.005 0.113 4928 Dihedral : 6.209 51.245 4588 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.25 % Favored : 92.63 % Rotamer: Outliers : 2.73 % Allowed : 21.08 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.92 (0.15), residues: 3392 helix: 0.38 (0.11), residues: 2208 sheet: -1.83 (0.36), residues: 196 loop : -2.55 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 832 TYR 0.015 0.001 TYR D 905 PHE 0.010 0.001 PHE D 921 TRP 0.053 0.002 TRP A 516 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00296 (29552) covalent geometry : angle 0.57869 (40032) SS BOND : bond 0.00659 ( 4) SS BOND : angle 2.28631 ( 8) hydrogen bonds : bond 0.03341 ( 1340) hydrogen bonds : angle 3.94430 ( 3984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 750 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8679 (pp30) cc_final: 0.8295 (pp30) REVERT: A 606 GLU cc_start: 0.8537 (pp20) cc_final: 0.8089 (pp20) REVERT: A 607 GLU cc_start: 0.8896 (tp30) cc_final: 0.8384 (tp30) REVERT: A 628 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8403 (mt-10) REVERT: A 646 ASN cc_start: 0.7466 (m-40) cc_final: 0.7182 (m110) REVERT: A 649 GLU cc_start: 0.8798 (mp0) cc_final: 0.8089 (mp0) REVERT: A 674 TYR cc_start: 0.8647 (m-80) cc_final: 0.8352 (m-80) REVERT: A 688 MET cc_start: 0.7622 (mtp) cc_final: 0.6340 (tmm) REVERT: A 773 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 779 MET cc_start: 0.8143 (tpp) cc_final: 0.7547 (ttm) REVERT: A 790 ASN cc_start: 0.9021 (m-40) cc_final: 0.8454 (t0) REVERT: A 798 PHE cc_start: 0.8771 (t80) cc_final: 0.8472 (t80) REVERT: A 808 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8230 (mm) REVERT: A 854 MET cc_start: 0.7775 (mmp) cc_final: 0.7535 (ptt) REVERT: A 955 LEU cc_start: 0.9330 (tp) cc_final: 0.9100 (tp) REVERT: A 977 GLN cc_start: 0.8695 (tp40) cc_final: 0.8116 (tp40) REVERT: A 987 GLN cc_start: 0.8418 (mp10) cc_final: 0.8217 (mp10) REVERT: B 297 GLN cc_start: 0.8677 (pp30) cc_final: 0.8302 (pp30) REVERT: B 553 GLN cc_start: 0.7490 (mp10) cc_final: 0.6826 (mm-40) REVERT: B 606 GLU cc_start: 0.8516 (pp20) cc_final: 0.8066 (pp20) REVERT: B 607 GLU cc_start: 0.8898 (tp30) cc_final: 0.8389 (tp30) REVERT: B 628 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 646 ASN cc_start: 0.7450 (m-40) cc_final: 0.7174 (m110) REVERT: B 649 GLU cc_start: 0.8829 (mp0) cc_final: 0.8122 (mp0) REVERT: B 674 TYR cc_start: 0.8655 (m-80) cc_final: 0.8364 (m-80) REVERT: B 688 MET cc_start: 0.7622 (mtp) cc_final: 0.6346 (tmm) REVERT: B 779 MET cc_start: 0.8311 (tpp) cc_final: 0.7460 (ttm) REVERT: B 790 ASN cc_start: 0.9024 (m-40) cc_final: 0.8527 (t0) REVERT: B 798 PHE cc_start: 0.8720 (t80) cc_final: 0.8424 (t80) REVERT: B 832 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8673 (mtp85) REVERT: B 841 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7657 (ttp80) REVERT: B 854 MET cc_start: 0.7916 (mmp) cc_final: 0.7602 (ptt) REVERT: B 898 TYR cc_start: 0.9383 (t80) cc_final: 0.8687 (t80) REVERT: B 955 LEU cc_start: 0.9327 (tp) cc_final: 0.9093 (tp) REVERT: B 977 GLN cc_start: 0.8696 (tp40) cc_final: 0.8117 (tp40) REVERT: B 987 GLN cc_start: 0.8393 (mp10) cc_final: 0.8188 (mp10) REVERT: C 297 GLN cc_start: 0.8680 (pp30) cc_final: 0.8296 (pp30) REVERT: C 553 GLN cc_start: 0.7656 (mp10) cc_final: 0.6852 (mp10) REVERT: C 606 GLU cc_start: 0.8522 (pp20) cc_final: 0.8075 (pp20) REVERT: C 607 GLU cc_start: 0.8889 (tp30) cc_final: 0.8384 (tp30) REVERT: C 628 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8409 (mt-10) REVERT: C 646 ASN cc_start: 0.7462 (m-40) cc_final: 0.7188 (m110) REVERT: C 649 GLU cc_start: 0.8836 (mp0) cc_final: 0.8134 (mp0) REVERT: C 674 TYR cc_start: 0.8644 (m-80) cc_final: 0.8347 (m-80) REVERT: C 688 MET cc_start: 0.7611 (mtp) cc_final: 0.6343 (tmm) REVERT: C 779 MET cc_start: 0.8312 (tpp) cc_final: 0.7460 (ttm) REVERT: C 789 TRP cc_start: 0.8681 (m100) cc_final: 0.8336 (m100) REVERT: C 790 ASN cc_start: 0.9001 (m-40) cc_final: 0.8433 (t0) REVERT: C 854 MET cc_start: 0.7904 (mmp) cc_final: 0.7598 (ptt) REVERT: C 898 TYR cc_start: 0.9385 (t80) cc_final: 0.8694 (t80) REVERT: C 955 LEU cc_start: 0.9327 (tp) cc_final: 0.9094 (tp) REVERT: C 977 GLN cc_start: 0.8698 (tp40) cc_final: 0.8130 (tp40) REVERT: C 987 GLN cc_start: 0.8398 (mp10) cc_final: 0.8193 (mp10) REVERT: D 297 GLN cc_start: 0.8673 (pp30) cc_final: 0.8333 (pp30) REVERT: D 553 GLN cc_start: 0.7655 (mp10) cc_final: 0.6865 (mp10) REVERT: D 606 GLU cc_start: 0.8520 (pp20) cc_final: 0.8071 (pp20) REVERT: D 607 GLU cc_start: 0.8893 (tp30) cc_final: 0.8387 (tp30) REVERT: D 628 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8404 (mt-10) REVERT: D 646 ASN cc_start: 0.7451 (m-40) cc_final: 0.7170 (m110) REVERT: D 649 GLU cc_start: 0.8823 (mp0) cc_final: 0.8116 (mp0) REVERT: D 674 TYR cc_start: 0.8643 (m-80) cc_final: 0.8343 (m-80) REVERT: D 688 MET cc_start: 0.7611 (mtp) cc_final: 0.6355 (tmm) REVERT: D 779 MET cc_start: 0.8308 (tpp) cc_final: 0.7451 (ttm) REVERT: D 790 ASN cc_start: 0.9043 (m-40) cc_final: 0.8515 (t0) REVERT: D 841 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7608 (ttp80) REVERT: D 854 MET cc_start: 0.7910 (mmp) cc_final: 0.7606 (ptt) REVERT: D 898 TYR cc_start: 0.9387 (t80) cc_final: 0.8613 (t80) REVERT: D 955 LEU cc_start: 0.9314 (tp) cc_final: 0.9067 (tp) REVERT: D 977 GLN cc_start: 0.8689 (tp40) cc_final: 0.8118 (tp40) REVERT: D 987 GLN cc_start: 0.8417 (mp10) cc_final: 0.8212 (mp10) REVERT: D 1068 MET cc_start: 0.4783 (ttt) cc_final: 0.3825 (mtt) outliers start: 85 outliers final: 66 residues processed: 799 average time/residue: 0.1707 time to fit residues: 223.4620 Evaluate side-chains 794 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 727 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 732 ASN Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 896 GLU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 732 ASN Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 268 optimal weight: 1.9990 chunk 328 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 207 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 159 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 915 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127770 restraints weight = 43968.947| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.89 r_work: 0.3328 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29556 Z= 0.120 Angle : 0.575 10.829 40040 Z= 0.297 Chirality : 0.042 0.315 4484 Planarity : 0.005 0.109 4928 Dihedral : 6.140 52.782 4588 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 2.83 % Allowed : 20.98 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.84 (0.15), residues: 3392 helix: 0.44 (0.11), residues: 2212 sheet: -1.79 (0.36), residues: 196 loop : -2.51 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 832 TYR 0.015 0.001 TYR D 905 PHE 0.011 0.001 PHE D 921 TRP 0.066 0.002 TRP A 516 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00286 (29552) covalent geometry : angle 0.57475 (40032) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.96157 ( 8) hydrogen bonds : bond 0.03332 ( 1340) hydrogen bonds : angle 3.91921 ( 3984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 778 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8720 (pp30) cc_final: 0.8355 (pp30) REVERT: A 553 GLN cc_start: 0.7703 (mp10) cc_final: 0.7493 (mp10) REVERT: A 600 ASN cc_start: 0.7931 (m110) cc_final: 0.7648 (m-40) REVERT: A 606 GLU cc_start: 0.8533 (pp20) cc_final: 0.8084 (pp20) REVERT: A 607 GLU cc_start: 0.8878 (tp30) cc_final: 0.8389 (tp30) REVERT: A 628 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 645 SER cc_start: 0.7518 (OUTLIER) cc_final: 0.6184 (t) REVERT: A 646 ASN cc_start: 0.7438 (m-40) cc_final: 0.7044 (m110) REVERT: A 649 GLU cc_start: 0.8793 (mp0) cc_final: 0.7950 (mp0) REVERT: A 674 TYR cc_start: 0.8633 (m-80) cc_final: 0.8333 (m-80) REVERT: A 688 MET cc_start: 0.7614 (mtp) cc_final: 0.6339 (tmm) REVERT: A 777 TRP cc_start: 0.7542 (t-100) cc_final: 0.6923 (t-100) REVERT: A 779 MET cc_start: 0.8080 (tpp) cc_final: 0.7267 (ttm) REVERT: A 785 PHE cc_start: 0.8549 (m-80) cc_final: 0.7924 (m-80) REVERT: A 790 ASN cc_start: 0.9026 (m-40) cc_final: 0.8528 (t0) REVERT: A 798 PHE cc_start: 0.8751 (t80) cc_final: 0.8437 (t80) REVERT: A 808 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 841 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7617 (ttp80) REVERT: A 955 LEU cc_start: 0.9332 (tp) cc_final: 0.9092 (tp) REVERT: A 977 GLN cc_start: 0.8663 (tp40) cc_final: 0.8129 (tp40) REVERT: A 1049 MET cc_start: 0.7987 (ptm) cc_final: 0.7764 (ttp) REVERT: B 297 GLN cc_start: 0.8719 (pp30) cc_final: 0.8360 (pp30) REVERT: B 553 GLN cc_start: 0.7567 (mp10) cc_final: 0.6916 (mm-40) REVERT: B 606 GLU cc_start: 0.8512 (pp20) cc_final: 0.8060 (pp20) REVERT: B 607 GLU cc_start: 0.8882 (tp30) cc_final: 0.8393 (tp30) REVERT: B 613 GLU cc_start: 0.8070 (tt0) cc_final: 0.7734 (tm-30) REVERT: B 628 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 645 SER cc_start: 0.7494 (OUTLIER) cc_final: 0.6147 (t) REVERT: B 646 ASN cc_start: 0.7456 (m-40) cc_final: 0.7073 (m110) REVERT: B 649 GLU cc_start: 0.8798 (mp0) cc_final: 0.7953 (mp0) REVERT: B 674 TYR cc_start: 0.8643 (m-80) cc_final: 0.8346 (m-80) REVERT: B 688 MET cc_start: 0.7612 (mtp) cc_final: 0.6340 (tmm) REVERT: B 777 TRP cc_start: 0.7535 (t-100) cc_final: 0.6924 (t-100) REVERT: B 779 MET cc_start: 0.8005 (tpp) cc_final: 0.7205 (ttm) REVERT: B 785 PHE cc_start: 0.8505 (m-80) cc_final: 0.7884 (m-80) REVERT: B 790 ASN cc_start: 0.9058 (m-40) cc_final: 0.8533 (t0) REVERT: B 798 PHE cc_start: 0.8742 (t80) cc_final: 0.8443 (t80) REVERT: B 832 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8597 (mtp85) REVERT: B 854 MET cc_start: 0.7980 (mmp) cc_final: 0.7645 (ptt) REVERT: B 898 TYR cc_start: 0.9372 (t80) cc_final: 0.8689 (t80) REVERT: B 955 LEU cc_start: 0.9320 (tp) cc_final: 0.9074 (tp) REVERT: B 977 GLN cc_start: 0.8651 (tp40) cc_final: 0.8115 (tp40) REVERT: B 1049 MET cc_start: 0.7973 (ptm) cc_final: 0.7715 (ttp) REVERT: C 297 GLN cc_start: 0.8686 (pp30) cc_final: 0.8298 (pp30) REVERT: C 553 GLN cc_start: 0.7558 (mp10) cc_final: 0.6747 (mp10) REVERT: C 606 GLU cc_start: 0.8508 (pp20) cc_final: 0.8061 (pp20) REVERT: C 607 GLU cc_start: 0.8878 (tp30) cc_final: 0.8396 (tp30) REVERT: C 613 GLU cc_start: 0.8050 (tt0) cc_final: 0.7727 (tm-30) REVERT: C 628 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8449 (mt-10) REVERT: C 645 SER cc_start: 0.7507 (OUTLIER) cc_final: 0.6190 (t) REVERT: C 646 ASN cc_start: 0.7450 (m-40) cc_final: 0.7079 (m110) REVERT: C 649 GLU cc_start: 0.8809 (mp0) cc_final: 0.7971 (mp0) REVERT: C 674 TYR cc_start: 0.8628 (m-80) cc_final: 0.8329 (m-80) REVERT: C 688 MET cc_start: 0.7624 (mtp) cc_final: 0.6338 (tmm) REVERT: C 777 TRP cc_start: 0.7548 (t-100) cc_final: 0.6900 (t-100) REVERT: C 779 MET cc_start: 0.8102 (tpp) cc_final: 0.7262 (ttm) REVERT: C 785 PHE cc_start: 0.8512 (m-80) cc_final: 0.7784 (m-80) REVERT: C 789 TRP cc_start: 0.8692 (m100) cc_final: 0.8385 (m100) REVERT: C 790 ASN cc_start: 0.9017 (m-40) cc_final: 0.8482 (t0) REVERT: C 841 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7584 (ttp80) REVERT: C 854 MET cc_start: 0.7966 (mmp) cc_final: 0.7635 (ptt) REVERT: C 887 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: C 898 TYR cc_start: 0.9372 (t80) cc_final: 0.8694 (t80) REVERT: C 955 LEU cc_start: 0.9338 (tp) cc_final: 0.9097 (tp) REVERT: C 977 GLN cc_start: 0.8682 (tp40) cc_final: 0.8100 (tp40) REVERT: C 1049 MET cc_start: 0.7975 (ptm) cc_final: 0.7744 (ttp) REVERT: D 297 GLN cc_start: 0.8659 (pp30) cc_final: 0.8320 (pp30) REVERT: D 553 GLN cc_start: 0.7667 (mp10) cc_final: 0.6881 (mp10) REVERT: D 606 GLU cc_start: 0.8507 (pp20) cc_final: 0.8059 (pp20) REVERT: D 607 GLU cc_start: 0.8877 (tp30) cc_final: 0.8393 (tp30) REVERT: D 613 GLU cc_start: 0.8041 (tt0) cc_final: 0.7709 (tm-30) REVERT: D 628 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8434 (mt-10) REVERT: D 645 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.6163 (t) REVERT: D 646 ASN cc_start: 0.7459 (m-40) cc_final: 0.7078 (m110) REVERT: D 649 GLU cc_start: 0.8803 (mp0) cc_final: 0.7963 (mp0) REVERT: D 674 TYR cc_start: 0.8631 (m-80) cc_final: 0.8331 (m-80) REVERT: D 688 MET cc_start: 0.7616 (mtp) cc_final: 0.6355 (tmm) REVERT: D 777 TRP cc_start: 0.7577 (t-100) cc_final: 0.7075 (t-100) REVERT: D 779 MET cc_start: 0.8029 (tpp) cc_final: 0.7220 (ttm) REVERT: D 785 PHE cc_start: 0.8516 (m-80) cc_final: 0.7790 (m-10) REVERT: D 790 ASN cc_start: 0.9050 (m-40) cc_final: 0.8511 (t0) REVERT: D 841 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7669 (ttp80) REVERT: D 854 MET cc_start: 0.7973 (mmp) cc_final: 0.7647 (ptt) REVERT: D 898 TYR cc_start: 0.9376 (t80) cc_final: 0.8691 (t80) REVERT: D 955 LEU cc_start: 0.9321 (tp) cc_final: 0.9063 (tp) REVERT: D 977 GLN cc_start: 0.8661 (tp40) cc_final: 0.8127 (tp40) REVERT: D 1049 MET cc_start: 0.7982 (ptm) cc_final: 0.7739 (ttp) REVERT: D 1068 MET cc_start: 0.4646 (ttt) cc_final: 0.3779 (mtt) outliers start: 88 outliers final: 68 residues processed: 826 average time/residue: 0.1741 time to fit residues: 232.3001 Evaluate side-chains 829 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 755 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 1073 ARG Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 896 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 342 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 334 optimal weight: 0.0980 chunk 221 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 732 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127119 restraints weight = 44036.549| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.91 r_work: 0.3315 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29556 Z= 0.132 Angle : 0.600 10.865 40040 Z= 0.309 Chirality : 0.043 0.330 4484 Planarity : 0.004 0.109 4928 Dihedral : 6.119 55.057 4588 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.84 % Favored : 93.04 % Rotamer: Outliers : 2.80 % Allowed : 21.27 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.74 (0.15), residues: 3392 helix: 0.51 (0.11), residues: 2220 sheet: -1.78 (0.36), residues: 196 loop : -2.47 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 832 TYR 0.018 0.001 TYR D 905 PHE 0.021 0.001 PHE D 921 TRP 0.066 0.002 TRP A 516 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00318 (29552) covalent geometry : angle 0.59950 (40032) SS BOND : bond 0.00496 ( 4) SS BOND : angle 1.90425 ( 8) hydrogen bonds : bond 0.03389 ( 1340) hydrogen bonds : angle 3.91361 ( 3984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 758 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8658 (pp30) cc_final: 0.8279 (pp30) REVERT: A 486 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8245 (mm-30) REVERT: A 600 ASN cc_start: 0.7917 (m110) cc_final: 0.7619 (m-40) REVERT: A 606 GLU cc_start: 0.8524 (pp20) cc_final: 0.8084 (pp20) REVERT: A 607 GLU cc_start: 0.8893 (tp30) cc_final: 0.8405 (tp30) REVERT: A 613 GLU cc_start: 0.8041 (tt0) cc_final: 0.7648 (tm-30) REVERT: A 628 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 645 SER cc_start: 0.7573 (OUTLIER) cc_final: 0.6164 (t) REVERT: A 646 ASN cc_start: 0.7423 (m-40) cc_final: 0.7035 (m110) REVERT: A 649 GLU cc_start: 0.8815 (mp0) cc_final: 0.7950 (mp0) REVERT: A 674 TYR cc_start: 0.8655 (m-80) cc_final: 0.8352 (m-80) REVERT: A 688 MET cc_start: 0.7601 (mtp) cc_final: 0.6317 (tmm) REVERT: A 777 TRP cc_start: 0.7802 (t-100) cc_final: 0.7061 (t-100) REVERT: A 779 MET cc_start: 0.8056 (tpp) cc_final: 0.7305 (ttm) REVERT: A 785 PHE cc_start: 0.8603 (m-80) cc_final: 0.7954 (m-80) REVERT: A 790 ASN cc_start: 0.8982 (m-40) cc_final: 0.8433 (t0) REVERT: A 798 PHE cc_start: 0.8771 (t80) cc_final: 0.8453 (t80) REVERT: A 808 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 841 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7561 (ttp80) REVERT: A 851 GLN cc_start: 0.8611 (mt0) cc_final: 0.8325 (mt0) REVERT: A 955 LEU cc_start: 0.9339 (tp) cc_final: 0.9090 (tp) REVERT: A 977 GLN cc_start: 0.8696 (tp40) cc_final: 0.8144 (tp40) REVERT: B 297 GLN cc_start: 0.8670 (pp30) cc_final: 0.8314 (pp30) REVERT: B 486 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 553 GLN cc_start: 0.7592 (mp10) cc_final: 0.6738 (mp10) REVERT: B 606 GLU cc_start: 0.8498 (pp20) cc_final: 0.8056 (pp20) REVERT: B 607 GLU cc_start: 0.8897 (tp30) cc_final: 0.8425 (tp30) REVERT: B 613 GLU cc_start: 0.8035 (tt0) cc_final: 0.7636 (tm-30) REVERT: B 628 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 645 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.6182 (t) REVERT: B 646 ASN cc_start: 0.7437 (m-40) cc_final: 0.7052 (m110) REVERT: B 649 GLU cc_start: 0.8809 (mp0) cc_final: 0.7941 (mp0) REVERT: B 674 TYR cc_start: 0.8657 (m-80) cc_final: 0.8348 (m-80) REVERT: B 688 MET cc_start: 0.7610 (mtp) cc_final: 0.6330 (tmm) REVERT: B 777 TRP cc_start: 0.7794 (t-100) cc_final: 0.7059 (t-100) REVERT: B 779 MET cc_start: 0.8075 (tpp) cc_final: 0.7308 (ttm) REVERT: B 785 PHE cc_start: 0.8572 (m-80) cc_final: 0.7882 (m-80) REVERT: B 790 ASN cc_start: 0.9052 (m-40) cc_final: 0.8548 (t0) REVERT: B 832 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8675 (mtp85) REVERT: B 854 MET cc_start: 0.7927 (mmp) cc_final: 0.7659 (ptt) REVERT: B 898 TYR cc_start: 0.9397 (t80) cc_final: 0.8707 (t80) REVERT: B 955 LEU cc_start: 0.9336 (tp) cc_final: 0.9086 (tp) REVERT: B 977 GLN cc_start: 0.8695 (tp40) cc_final: 0.8139 (tp40) REVERT: C 297 GLN cc_start: 0.8695 (pp30) cc_final: 0.8320 (pp30) REVERT: C 486 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8225 (mm-30) REVERT: C 553 GLN cc_start: 0.7565 (mp10) cc_final: 0.6790 (mp10) REVERT: C 606 GLU cc_start: 0.8493 (pp20) cc_final: 0.8054 (pp20) REVERT: C 607 GLU cc_start: 0.8900 (tp30) cc_final: 0.8428 (tp30) REVERT: C 613 GLU cc_start: 0.8040 (tt0) cc_final: 0.7695 (tm-30) REVERT: C 628 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8382 (mt-10) REVERT: C 645 SER cc_start: 0.7594 (OUTLIER) cc_final: 0.6231 (t) REVERT: C 646 ASN cc_start: 0.7420 (m-40) cc_final: 0.7051 (m110) REVERT: C 649 GLU cc_start: 0.8813 (mp0) cc_final: 0.7949 (mp0) REVERT: C 674 TYR cc_start: 0.8641 (m-80) cc_final: 0.8328 (m-80) REVERT: C 688 MET cc_start: 0.7603 (mtp) cc_final: 0.6323 (tmm) REVERT: C 777 TRP cc_start: 0.7819 (t-100) cc_final: 0.7065 (t-100) REVERT: C 779 MET cc_start: 0.8082 (tpp) cc_final: 0.7309 (ttm) REVERT: C 785 PHE cc_start: 0.8574 (m-80) cc_final: 0.7871 (m-80) REVERT: C 789 TRP cc_start: 0.8683 (m100) cc_final: 0.8374 (m100) REVERT: C 790 ASN cc_start: 0.8983 (m-40) cc_final: 0.8436 (t0) REVERT: C 854 MET cc_start: 0.7909 (mmp) cc_final: 0.7654 (ptt) REVERT: C 887 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: C 898 TYR cc_start: 0.9391 (t80) cc_final: 0.8710 (t80) REVERT: C 955 LEU cc_start: 0.9335 (tp) cc_final: 0.9085 (tp) REVERT: C 977 GLN cc_start: 0.8720 (tp40) cc_final: 0.8163 (tp40) REVERT: D 297 GLN cc_start: 0.8669 (pp30) cc_final: 0.8324 (pp30) REVERT: D 486 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 553 GLN cc_start: 0.7498 (mp10) cc_final: 0.6692 (mp10) REVERT: D 606 GLU cc_start: 0.8490 (pp20) cc_final: 0.8048 (pp20) REVERT: D 607 GLU cc_start: 0.8903 (tp30) cc_final: 0.8431 (tp30) REVERT: D 613 GLU cc_start: 0.8005 (tt0) cc_final: 0.7654 (tm-30) REVERT: D 628 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 645 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.6206 (t) REVERT: D 646 ASN cc_start: 0.7448 (m-40) cc_final: 0.7063 (m110) REVERT: D 649 GLU cc_start: 0.8823 (mp0) cc_final: 0.7971 (mp0) REVERT: D 674 TYR cc_start: 0.8644 (m-80) cc_final: 0.8331 (m-80) REVERT: D 688 MET cc_start: 0.7610 (mtp) cc_final: 0.6336 (tmm) REVERT: D 777 TRP cc_start: 0.7815 (t-100) cc_final: 0.7066 (t-100) REVERT: D 779 MET cc_start: 0.8071 (tpp) cc_final: 0.7298 (ttm) REVERT: D 785 PHE cc_start: 0.8578 (m-80) cc_final: 0.7768 (m-80) REVERT: D 790 ASN cc_start: 0.8974 (m-40) cc_final: 0.8377 (t0) REVERT: D 841 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7705 (ttp80) REVERT: D 854 MET cc_start: 0.7923 (mmp) cc_final: 0.7640 (ptt) REVERT: D 898 TYR cc_start: 0.9398 (t80) cc_final: 0.8701 (t80) REVERT: D 955 LEU cc_start: 0.9335 (tp) cc_final: 0.9075 (tp) REVERT: D 977 GLN cc_start: 0.8697 (tp40) cc_final: 0.8142 (tp40) REVERT: D 1068 MET cc_start: 0.4550 (ttt) cc_final: 0.3765 (mtp) outliers start: 87 outliers final: 78 residues processed: 799 average time/residue: 0.1702 time to fit residues: 221.1087 Evaluate side-chains 824 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 740 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 732 ASN Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1073 ARG Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 417 TRP Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 896 GLU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 732 ASN Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 97 optimal weight: 0.2980 chunk 246 optimal weight: 0.0070 chunk 300 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 158 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 600 ASN A 915 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS B 600 ASN B 915 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN C 915 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 ASN D 915 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128817 restraints weight = 43713.435| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.87 r_work: 0.3350 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29556 Z= 0.117 Angle : 0.596 10.764 40040 Z= 0.304 Chirality : 0.042 0.283 4484 Planarity : 0.004 0.101 4928 Dihedral : 6.066 56.582 4588 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 2.54 % Allowed : 21.72 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.64 (0.15), residues: 3392 helix: 0.59 (0.11), residues: 2212 sheet: -1.75 (0.36), residues: 196 loop : -2.43 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 832 TYR 0.019 0.001 TYR C 905 PHE 0.021 0.001 PHE A 921 TRP 0.063 0.002 TRP A 516 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00277 (29552) covalent geometry : angle 0.59535 (40032) SS BOND : bond 0.00484 ( 4) SS BOND : angle 1.82877 ( 8) hydrogen bonds : bond 0.03319 ( 1340) hydrogen bonds : angle 3.87727 ( 3984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 773 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8674 (pp30) cc_final: 0.8378 (pp30) REVERT: A 607 GLU cc_start: 0.8884 (tp30) cc_final: 0.8402 (tp30) REVERT: A 613 GLU cc_start: 0.7954 (tt0) cc_final: 0.7621 (tm-30) REVERT: A 628 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8407 (mt-10) REVERT: A 645 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.6222 (t) REVERT: A 646 ASN cc_start: 0.7351 (m-40) cc_final: 0.6989 (m110) REVERT: A 649 GLU cc_start: 0.8769 (mp0) cc_final: 0.7941 (mp0) REVERT: A 688 MET cc_start: 0.7612 (mtp) cc_final: 0.6317 (tmm) REVERT: A 777 TRP cc_start: 0.7813 (t-100) cc_final: 0.7155 (t-100) REVERT: A 779 MET cc_start: 0.8033 (tpp) cc_final: 0.7331 (ttm) REVERT: A 785 PHE cc_start: 0.8578 (m-80) cc_final: 0.7969 (m-80) REVERT: A 790 ASN cc_start: 0.9011 (m-40) cc_final: 0.8495 (t0) REVERT: A 808 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8248 (mm) REVERT: A 904 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 955 LEU cc_start: 0.9341 (tp) cc_final: 0.9099 (tp) REVERT: A 977 GLN cc_start: 0.8661 (tp40) cc_final: 0.8097 (tp40) REVERT: B 297 GLN cc_start: 0.8661 (pp30) cc_final: 0.8370 (pp30) REVERT: B 553 GLN cc_start: 0.7566 (mp10) cc_final: 0.6739 (mp10) REVERT: B 607 GLU cc_start: 0.8880 (tp30) cc_final: 0.8397 (tp30) REVERT: B 613 GLU cc_start: 0.7971 (tt0) cc_final: 0.7638 (tm-30) REVERT: B 628 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8399 (mt-10) REVERT: B 645 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.6516 (t) REVERT: B 649 GLU cc_start: 0.8769 (mp0) cc_final: 0.8066 (mp0) REVERT: B 688 MET cc_start: 0.7608 (mtp) cc_final: 0.6327 (tmm) REVERT: B 777 TRP cc_start: 0.7824 (t-100) cc_final: 0.7146 (t-100) REVERT: B 779 MET cc_start: 0.8067 (tpp) cc_final: 0.7333 (ttm) REVERT: B 785 PHE cc_start: 0.8533 (m-80) cc_final: 0.7891 (m-80) REVERT: B 790 ASN cc_start: 0.9045 (m-40) cc_final: 0.8631 (t0) REVERT: B 832 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8604 (mtp85) REVERT: B 854 MET cc_start: 0.7943 (mmp) cc_final: 0.7685 (ptt) REVERT: B 898 TYR cc_start: 0.9353 (t80) cc_final: 0.8697 (t80) REVERT: B 955 LEU cc_start: 0.9334 (tp) cc_final: 0.9095 (tp) REVERT: B 977 GLN cc_start: 0.8654 (tp40) cc_final: 0.8095 (tp40) REVERT: B 1049 MET cc_start: 0.7964 (ptm) cc_final: 0.7620 (ttp) REVERT: C 297 GLN cc_start: 0.8661 (pp30) cc_final: 0.8351 (pp30) REVERT: C 553 GLN cc_start: 0.7571 (mp10) cc_final: 0.6827 (mp10) REVERT: C 607 GLU cc_start: 0.8884 (tp30) cc_final: 0.8403 (tp30) REVERT: C 613 GLU cc_start: 0.7955 (tt0) cc_final: 0.7628 (tm-30) REVERT: C 628 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 645 SER cc_start: 0.7539 (OUTLIER) cc_final: 0.6549 (t) REVERT: C 649 GLU cc_start: 0.8789 (mp0) cc_final: 0.8093 (mp0) REVERT: C 688 MET cc_start: 0.7605 (mtp) cc_final: 0.6323 (tmm) REVERT: C 777 TRP cc_start: 0.7837 (t-100) cc_final: 0.7176 (t-100) REVERT: C 779 MET cc_start: 0.8081 (tpp) cc_final: 0.7349 (ttm) REVERT: C 785 PHE cc_start: 0.8548 (m-80) cc_final: 0.7843 (m-80) REVERT: C 789 TRP cc_start: 0.8640 (m100) cc_final: 0.8388 (m100) REVERT: C 790 ASN cc_start: 0.9013 (m-40) cc_final: 0.8509 (t0) REVERT: C 854 MET cc_start: 0.7926 (mmp) cc_final: 0.7681 (ptt) REVERT: C 887 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: C 898 TYR cc_start: 0.9350 (t80) cc_final: 0.8701 (t80) REVERT: C 955 LEU cc_start: 0.9338 (tp) cc_final: 0.9097 (tp) REVERT: C 977 GLN cc_start: 0.8692 (tp40) cc_final: 0.8091 (tp40) REVERT: D 297 GLN cc_start: 0.8652 (pp30) cc_final: 0.8331 (pp30) REVERT: D 553 GLN cc_start: 0.7646 (mp10) cc_final: 0.6917 (mp10) REVERT: D 607 GLU cc_start: 0.8874 (tp30) cc_final: 0.8395 (tp30) REVERT: D 613 GLU cc_start: 0.7946 (tt0) cc_final: 0.7617 (tm-30) REVERT: D 628 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8414 (mt-10) REVERT: D 645 SER cc_start: 0.7528 (OUTLIER) cc_final: 0.6525 (t) REVERT: D 649 GLU cc_start: 0.8770 (mp0) cc_final: 0.8073 (mp0) REVERT: D 688 MET cc_start: 0.7617 (mtp) cc_final: 0.6335 (tmm) REVERT: D 777 TRP cc_start: 0.7843 (t-100) cc_final: 0.7183 (t-100) REVERT: D 779 MET cc_start: 0.8062 (tpp) cc_final: 0.7320 (ttm) REVERT: D 785 PHE cc_start: 0.8567 (m-80) cc_final: 0.7849 (m-80) REVERT: D 790 ASN cc_start: 0.8919 (m-40) cc_final: 0.8411 (t0) REVERT: D 841 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7605 (ttp80) REVERT: D 854 MET cc_start: 0.7912 (mmp) cc_final: 0.7660 (ptt) REVERT: D 898 TYR cc_start: 0.9358 (t80) cc_final: 0.8691 (t80) REVERT: D 955 LEU cc_start: 0.9306 (tp) cc_final: 0.9028 (tp) REVERT: D 977 GLN cc_start: 0.8671 (tp40) cc_final: 0.8116 (tp40) REVERT: D 1068 MET cc_start: 0.4446 (ttt) cc_final: 0.3682 (mtp) outliers start: 79 outliers final: 60 residues processed: 813 average time/residue: 0.1738 time to fit residues: 230.6346 Evaluate side-chains 792 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 726 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 915 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1073 ARG Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 915 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 270 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 285 optimal weight: 0.4980 chunk 231 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 266 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.159780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129086 restraints weight = 44060.989| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.86 r_work: 0.3351 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 29556 Z= 0.184 Angle : 0.808 59.200 40040 Z= 0.462 Chirality : 0.042 0.250 4484 Planarity : 0.004 0.100 4928 Dihedral : 6.080 56.609 4588 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 2.22 % Allowed : 22.91 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.63 (0.15), residues: 3392 helix: 0.60 (0.11), residues: 2212 sheet: -1.75 (0.36), residues: 196 loop : -2.42 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 832 TYR 0.017 0.001 TYR C 905 PHE 0.011 0.001 PHE A 921 TRP 0.057 0.002 TRP A 516 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00373 (29552) covalent geometry : angle 0.80719 (40032) SS BOND : bond 0.00567 ( 4) SS BOND : angle 1.84035 ( 8) hydrogen bonds : bond 0.03329 ( 1340) hydrogen bonds : angle 3.87850 ( 3984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6463.75 seconds wall clock time: 111 minutes 41.60 seconds (6701.60 seconds total)