Starting phenix.real_space_refine on Tue Aug 26 14:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eu3_3958/08_2025/6eu3_3958_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eu3_3958/08_2025/6eu3_3958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6eu3_3958/08_2025/6eu3_3958_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eu3_3958/08_2025/6eu3_3958_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6eu3_3958/08_2025/6eu3_3958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eu3_3958/08_2025/6eu3_3958.map" } resolution = 3.3 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 207 5.16 5 C 24312 2.51 5 N 6586 2.21 5 O 7218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38330 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 10980 Classifications: {'peptide': 1402} Link IDs: {'PTRANS': 63, 'TRANS': 1338} Chain breaks: 3 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 558 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "O" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4316 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 17, 'TRANS': 519} Chain breaks: 2 Chain: "P" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "Q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 74.419 65.509 80.944 1.00 71.80 S ATOM 510 SG CYS A 70 77.933 66.708 79.240 1.00 63.74 S ATOM 557 SG CYS A 77 78.581 64.324 81.979 1.00 54.56 S ATOM 795 SG CYS A 107 61.114 111.700 95.728 1.00 41.04 S ATOM 1184 SG CYS A 154 62.450 114.613 93.891 1.00 63.69 S ATOM 1208 SG CYS A 157 58.713 113.852 93.980 1.00 54.90 S ATOM 19341 SG CYS B1095 81.199 82.749 75.285 1.00 27.39 S ATOM 19364 SG CYS B1098 77.396 85.877 75.129 1.00 25.16 S ATOM 19430 SG CYS B1107 78.128 81.107 74.439 1.00 47.09 S ATOM 28892 SG CYS J 10 130.526 38.838 124.635 1.00 24.19 S ATOM 29172 SG CYS J 45 128.143 42.237 127.218 1.00 21.97 S ATOM 29178 SG CYS J 46 128.589 38.296 127.603 1.00 18.86 S ATOM 30215 SG CYS L 31 85.523 24.781 122.758 1.00 31.17 S ATOM 30235 SG CYS L 34 85.544 21.372 124.054 1.00 37.92 S ATOM 30339 SG CYS L 48 82.684 24.328 120.622 1.00 49.63 S ATOM 30362 SG CYS L 51 82.420 23.680 124.854 1.00 48.73 S Time building chain proxies: 8.94, per 1000 atoms: 0.23 Number of scatterers: 38330 At special positions: 0 Unit cell: (189, 159.6, 206.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 207 16.00 Mg 1 11.99 O 7218 8.00 N 6586 7.00 C 24312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 6 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9116 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 46 sheets defined 33.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.768A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.821A pdb=" N GLY A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.518A pdb=" N ARG A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.835A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 208 removed outlier: 4.337A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.662A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.844A pdb=" N GLU A 240 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 305 removed outlier: 4.024A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 327 removed outlier: 4.187A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 4.227A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.857A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.555A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.549A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.781A pdb=" N THR A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 4.066A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 709 removed outlier: 3.564A pdb=" N THR A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Proline residue: A 687 - end of helix removed outlier: 3.890A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 746 removed outlier: 3.607A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.652A pdb=" N LYS A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.621A pdb=" N ALA A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 810 removed outlier: 3.500A pdb=" N VAL A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.706A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.694A pdb=" N THR A 882 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.543A pdb=" N ASP A 919 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.947A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 963 removed outlier: 3.665A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.705A pdb=" N ASP A 988 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 989 " --> pdb=" O ARG A 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 989' Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.869A pdb=" N LYS A1015 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1058 removed outlier: 3.629A pdb=" N SER A1055 " --> pdb=" O ASN A1051 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A1057 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A1058 " --> pdb=" O THR A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1080 removed outlier: 3.535A pdb=" N VAL A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.902A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1104 removed outlier: 3.682A pdb=" N GLN A1103 " --> pdb=" O PRO A1100 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A1104 " --> pdb=" O GLY A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1100 through 1104' Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1151 through 1160 removed outlier: 3.553A pdb=" N ARG A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A1159 " --> pdb=" O ARG A1155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 removed outlier: 3.639A pdb=" N VAL A1169 " --> pdb=" O LEU A1165 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A1170 " --> pdb=" O LEU A1166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1170' Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1255 through 1266 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.508A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.566A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A1343 " --> pdb=" O ILE A1339 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.792A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 Processing helix chain 'A' and resid 1394 through 1403 removed outlier: 4.047A pdb=" N ASP A1398 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1399 " --> pdb=" O HIS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1457 removed outlier: 3.973A pdb=" N ALA A1456 " --> pdb=" O ASN A1453 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1457 " --> pdb=" O GLU A1454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1453 through 1457' Processing helix chain 'B' and resid 42 through 45 removed outlier: 3.572A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.768A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 4.322A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.284A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.602A pdb=" N LEU B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 279 through 289 removed outlier: 5.478A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.524A pdb=" N TYR B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.767A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.898A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 440 removed outlier: 4.003A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.659A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.631A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 526 through 536 removed outlier: 4.219A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.778A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.842A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 643 " --> pdb=" O ASP B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.849A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 681' Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.910A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.031A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 4.297A pdb=" N ASP B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 969 removed outlier: 3.607A pdb=" N LEU B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.668A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.760A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B1073 " --> pdb=" O CYS B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 4.038A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 Processing helix chain 'B' and resid 1123 through 1135 removed outlier: 3.746A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.586A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 4.188A pdb=" N PHE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.541A pdb=" N ILE C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.524A pdb=" N MET C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 113' Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.643A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.661A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.680A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 273 " --> pdb=" O ALA C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 269 through 273' Processing helix chain 'C' and resid 309 through 327 removed outlier: 3.674A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.989A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.579A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 117 through 125 removed outlier: 4.396A pdb=" N LEU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.516A pdb=" N TYR D 135 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.578A pdb=" N ILE D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.860A pdb=" N GLU E 6 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 27 removed outlier: 3.639A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 4.441A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.737A pdb=" N MET E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 59' Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.652A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.789A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.639A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.513A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.530A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.687A pdb=" N ASN G 32 " --> pdb=" O HIS G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.765A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.586A pdb=" N GLU J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.746A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.843A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.940A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 137 Processing helix chain 'M' and resid 184 through 193 Processing helix chain 'M' and resid 231 through 236 Processing helix chain 'N' and resid 277 through 282 removed outlier: 3.586A pdb=" N LEU N 282 " --> pdb=" O ALA N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 295 removed outlier: 3.739A pdb=" N HIS N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS N 289 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 55 removed outlier: 3.809A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 72 removed outlier: 3.640A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 3.521A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.798A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR O 94 " --> pdb=" O SER O 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 133 removed outlier: 3.668A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 159 through 167 Processing helix chain 'O' and resid 185 through 195 removed outlier: 3.784A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS O 195 " --> pdb=" O PHE O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 222 removed outlier: 3.521A pdb=" N LEU O 214 " --> pdb=" O PRO O 210 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 254 removed outlier: 5.238A pdb=" N LYS O 242 " --> pdb=" O ARG O 238 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.856A pdb=" N LYS O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER O 293 " --> pdb=" O LYS O 289 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 338 through 355 removed outlier: 4.150A pdb=" N GLN O 346 " --> pdb=" O ALA O 342 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP O 347 " --> pdb=" O LYS O 343 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU O 350 " --> pdb=" O GLN O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 367 removed outlier: 3.610A pdb=" N LEU O 366 " --> pdb=" O ALA O 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA O 367 " --> pdb=" O ILE O 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 363 through 367' Processing helix chain 'O' and resid 451 through 462 Processing helix chain 'O' and resid 483 through 500 removed outlier: 3.671A pdb=" N VAL O 491 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR O 492 " --> pdb=" O LYS O 488 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL O 495 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE O 496 " --> pdb=" O TYR O 492 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.954A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 532 through 542 removed outlier: 3.529A pdb=" N LEU O 537 " --> pdb=" O ILE O 533 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA O 538 " --> pdb=" O ARG O 534 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER O 539 " --> pdb=" O SER O 535 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 593 removed outlier: 3.573A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS O 592 " --> pdb=" O LEU O 588 " (cutoff:3.500A) Processing helix chain 'O' and resid 594 through 599 removed outlier: 3.518A pdb=" N GLU O 598 " --> pdb=" O LEU O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 626 through 649 removed outlier: 3.521A pdb=" N ASN O 631 " --> pdb=" O LEU O 627 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU O 632 " --> pdb=" O LYS O 628 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG O 633 " --> pdb=" O MET O 629 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL O 637 " --> pdb=" O ARG O 633 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG O 640 " --> pdb=" O ASN O 636 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 653 removed outlier: 3.726A pdb=" N MET O 653 " --> pdb=" O VAL O 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 650 through 653' Processing helix chain 'P' and resid 172 through 190 removed outlier: 4.023A pdb=" N ASN P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 219 through 227 Processing helix chain 'P' and resid 239 through 248 Processing helix chain 'P' and resid 256 through 260 removed outlier: 3.936A pdb=" N CYS P 260 " --> pdb=" O THR P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.761A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 67 removed outlier: 3.800A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.062A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 3.556A pdb=" N LEU A 86 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.756A pdb=" N ALA A 112 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.232A pdb=" N HIS A 180 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372 removed outlier: 4.224A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.583A pdb=" N LYS A 491 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 499 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.059A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.138A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.532A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AB3, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AB4, first strand: chain 'A' and resid 1281 through 1285 Processing sheet with id=AB5, first strand: chain 'A' and resid 1429 through 1431 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.980A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR B 135 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS B 144 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.475A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.095A pdb=" N LYS B 228 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.833A pdb=" N LEU B 242 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE B 251 " --> pdb=" O LEU B 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.570A pdb=" N TRP B 442 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG B 451 " --> pdb=" O TRP B 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC5, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AC6, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.842A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.842A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.882A pdb=" N GLN B1025 " --> pdb=" O SER B 913 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU B 771 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL B 926 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 773 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 772 " --> pdb=" O ILE B 943 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 943 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 758 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.369A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD2, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD3, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.766A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.683A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.012A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.652A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 230 through 234 removed outlier: 4.127A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.686A pdb=" N LYS D 2 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.523A pdb=" N GLU E 81 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 111 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.176A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 88 through 91 removed outlier: 7.317A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 97 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 95 through 96 removed outlier: 5.340A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 13 through 16 removed outlier: 3.636A pdb=" N LEU I 13 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.642A pdb=" N GLN K 64 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.558A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 84 through 87 removed outlier: 4.533A pdb=" N SER M 84 " --> pdb=" O ILE N 399 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE N 399 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER N 398 " --> pdb=" O GLU N 407 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU N 407 " --> pdb=" O SER N 398 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 104 through 109 Processing sheet with id=AE9, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AF1, first strand: chain 'O' and resid 548 through 552 1079 hydrogen bonds defined for protein. 3045 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: 9.11 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12474 1.34 - 1.46: 7862 1.46 - 1.58: 18342 1.58 - 1.70: 1 1.70 - 1.82: 337 Bond restraints: 39016 Sorted by residual: bond pdb=" CA VAL E 124 " pdb=" CB VAL E 124 " ideal model delta sigma weight residual 1.534 1.554 -0.020 6.80e-03 2.16e+04 8.38e+00 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.340 1.418 -0.078 2.76e-02 1.31e+03 7.96e+00 bond pdb=" C ALA P 209 " pdb=" N PRO P 210 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.33e-02 5.65e+03 7.86e+00 bond pdb=" C GLY P 201 " pdb=" N PRO P 202 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.65e+00 bond pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.80e+00 ... (remaining 39011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 51925 3.66 - 7.33: 641 7.33 - 10.99: 111 10.99 - 14.65: 9 14.65 - 18.31: 1 Bond angle restraints: 52687 Sorted by residual: angle pdb=" N LEU N 409 " pdb=" CA LEU N 409 " pdb=" C LEU N 409 " ideal model delta sigma weight residual 110.80 92.49 18.31 2.13e+00 2.20e-01 7.39e+01 angle pdb=" C GLN A 275 " pdb=" N ASP A 276 " pdb=" CA ASP A 276 " ideal model delta sigma weight residual 121.54 134.69 -13.15 1.91e+00 2.74e-01 4.74e+01 angle pdb=" C ILE Q 43 " pdb=" N ASN Q 44 " pdb=" CA ASN Q 44 " ideal model delta sigma weight residual 121.54 133.49 -11.95 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C GLU P 308 " pdb=" N VAL P 309 " pdb=" CA VAL P 309 " ideal model delta sigma weight residual 121.97 132.97 -11.00 1.80e+00 3.09e-01 3.74e+01 angle pdb=" N ILE B 324 " pdb=" CA ILE B 324 " pdb=" C ILE B 324 " ideal model delta sigma weight residual 113.53 107.95 5.58 9.80e-01 1.04e+00 3.24e+01 ... (remaining 52682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 22318 15.97 - 31.94: 1225 31.94 - 47.91: 363 47.91 - 63.88: 23 63.88 - 79.85: 30 Dihedral angle restraints: 23959 sinusoidal: 9879 harmonic: 14080 Sorted by residual: dihedral pdb=" CA LYS P 307 " pdb=" C LYS P 307 " pdb=" N GLU P 308 " pdb=" CA GLU P 308 " ideal model delta harmonic sigma weight residual -180.00 -100.15 -79.85 0 5.00e+00 4.00e-02 2.55e+02 dihedral pdb=" CA GLU P 308 " pdb=" C GLU P 308 " pdb=" N VAL P 309 " pdb=" CA VAL P 309 " ideal model delta harmonic sigma weight residual -180.00 -110.89 -69.11 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA LYS B 583 " pdb=" C LYS B 583 " pdb=" N VAL B 584 " pdb=" CA VAL B 584 " ideal model delta harmonic sigma weight residual -180.00 -121.12 -58.88 0 5.00e+00 4.00e-02 1.39e+02 ... (remaining 23956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5111 0.082 - 0.164: 770 0.164 - 0.246: 68 0.246 - 0.328: 8 0.328 - 0.410: 4 Chirality restraints: 5961 Sorted by residual: chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILE A 712 " pdb=" CA ILE A 712 " pdb=" CG1 ILE A 712 " pdb=" CG2 ILE A 712 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB VAL B 888 " pdb=" CA VAL B 888 " pdb=" CG1 VAL B 888 " pdb=" CG2 VAL B 888 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 5958 not shown) Planarity restraints: 6778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER O 239 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C SER O 239 " -0.060 2.00e-02 2.50e+03 pdb=" O SER O 239 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN O 240 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS O 236 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LYS O 236 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS O 236 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS O 237 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 28 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C LYS L 28 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS L 28 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR L 29 " -0.018 2.00e-02 2.50e+03 ... (remaining 6775 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 2 1.91 - 2.66: 501 2.66 - 3.41: 49828 3.41 - 4.15: 85268 4.15 - 4.90: 154247 Nonbonded interactions: 289846 Sorted by model distance: nonbonded pdb=" CZ PHE N 304 " pdb=" CD2 LEU N 409 " model vdw 1.167 3.760 nonbonded pdb=" CE2 PHE N 304 " pdb=" CD2 LEU N 409 " model vdw 1.635 3.760 nonbonded pdb=" CE1 PHE N 304 " pdb=" CD2 LEU N 409 " model vdw 2.133 3.760 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A2002 " model vdw 2.143 2.170 nonbonded pdb=" O SER I 28 " pdb=" OH TYR M 185 " model vdw 2.245 3.040 ... (remaining 289841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 39.670 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0373 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 : 0.008 0.671 39032 Z= 0.316 Angle : 1.096 42.448 52693 Z= 0.563 Chirality : 0.059 0.410 5961 Planarity : 0.007 0.072 6778 Dihedral : 11.408 79.855 14843 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.89 % Favored : 86.61 % Rotamer: Outliers : 0.26 % Allowed : 6.52 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 1.92 % Twisted General : 0.70 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.18 (0.09), residues: 4765 helix: -3.81 (0.08), residues: 1517 sheet: -2.12 (0.20), residues: 558 loop : -3.65 (0.09), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 915 TYR 0.030 0.002 TYR P 249 PHE 0.031 0.002 PHE B1018 TRP 0.037 0.003 TRP O 583 HIS 0.015 0.002 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00445 (39016) covalent geometry : angle 1.06403 (52687) hydrogen bonds : bond 0.22970 ( 1058) hydrogen bonds : angle 8.42284 ( 3045) metal coordination : bond 0.33353 ( 16) metal coordination : angle 24.47908 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 563 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.0867 (ttmt) cc_final: 0.0367 (mttt) REVERT: A 229 ASN cc_start: 0.3094 (m-40) cc_final: 0.0374 (p0) REVERT: A 326 TYR cc_start: 0.3424 (t80) cc_final: 0.2608 (t80) REVERT: A 427 HIS cc_start: 0.1644 (t-90) cc_final: 0.1220 (t-90) REVERT: A 742 ILE cc_start: -0.0420 (mm) cc_final: -0.0696 (tt) REVERT: A 774 ARG cc_start: -0.0086 (ppp80) cc_final: -0.1128 (ppp80) REVERT: A 1389 PHE cc_start: 0.3464 (t80) cc_final: 0.1952 (p90) REVERT: B 123 MET cc_start: -0.2480 (mtp) cc_final: -0.3149 (pmm) REVERT: B 188 ASN cc_start: 0.0660 (t0) cc_final: -0.0064 (t0) REVERT: B 405 LYS cc_start: 0.6451 (ttpp) cc_final: 0.6048 (mttm) REVERT: B 479 LYS cc_start: 0.2195 (pmtt) cc_final: 0.1829 (pttt) REVERT: B 935 ASP cc_start: 0.3158 (p0) cc_final: 0.2297 (t0) REVERT: B 1137 ILE cc_start: 0.0869 (mt) cc_final: 0.0596 (mt) REVERT: E 28 TYR cc_start: 0.2578 (m-10) cc_final: 0.1771 (m-80) REVERT: G 144 GLU cc_start: 0.3252 (pp20) cc_final: 0.2237 (pt0) REVERT: I 1 MET cc_start: 0.2096 (mmm) cc_final: 0.0802 (ptt) REVERT: K 121 LEU cc_start: -0.0498 (tp) cc_final: -0.0885 (pp) REVERT: N 305 MET cc_start: 0.0817 (mpt) cc_final: -0.0878 (mtm) REVERT: O 105 LYS cc_start: 0.3392 (mmtp) cc_final: 0.2742 (mttp) REVERT: O 500 LEU cc_start: 0.3965 (tp) cc_final: 0.3259 (tp) REVERT: P 175 ILE cc_start: 0.6034 (mt) cc_final: 0.5308 (tt) REVERT: P 239 ASN cc_start: 0.4786 (p0) cc_final: 0.4507 (m-40) outliers start: 11 outliers final: 2 residues processed: 574 average time/residue: 0.2491 time to fit residues: 232.0091 Evaluate side-chains 344 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 342 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain J residue 2 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.0970 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 161 ASN A 229 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 533 ASN A 566 HIS A 618 HIS A 643 ASN A 808 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN A 948 ASN A 990 ASN A1142 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN A1254 ASN A1354 HIS A1419 GLN A1453 ASN B 39 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN B 490 GLN B 626 HIS ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 800 ASN B 803 GLN B 840 GLN B 861 ASN B 893 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 ASN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 997 ASN B1025 GLN B1049 GLN C 137 ASN C 143 ASN C 207 HIS D 71 ASN D 133 HIS E 5 ASN E 32 GLN E 54 GLN E 101 GLN E 136 ASN G 36 ASN H 33 GLN H 128 ASN I 10 ASN K 95 HIS ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS M 155 ASN M 158 GLN M 190 ASN N 298 ASN O 202 GLN O 244 ASN O 254 ASN O 310 GLN O 346 GLN O 362 ASN O 369 HIS O 464 ASN O 544 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 572 HIS O 652 GLN ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.224321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.191554 restraints weight = 56304.502| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.09 r_work: 0.4039 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1066 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 39032 Z= 0.166 Angle : 0.785 16.810 52693 Z= 0.403 Chirality : 0.047 0.260 5961 Planarity : 0.006 0.087 6778 Dihedral : 6.733 74.059 5230 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.19 % Favored : 87.47 % Rotamer: Outliers : 2.09 % Allowed : 9.40 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.08 (0.10), residues: 4765 helix: -2.41 (0.11), residues: 1526 sheet: -1.66 (0.22), residues: 529 loop : -3.24 (0.10), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 368 TYR 0.028 0.002 TYR L 29 PHE 0.030 0.002 PHE I 33 TRP 0.025 0.002 TRP E 79 HIS 0.014 0.002 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00357 (39016) covalent geometry : angle 0.78050 (52687) hydrogen bonds : bond 0.04542 ( 1058) hydrogen bonds : angle 5.57901 ( 3045) metal coordination : bond 0.01652 ( 16) metal coordination : angle 7.89637 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 398 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TRP cc_start: 0.4830 (t60) cc_final: 0.4192 (t60) REVERT: A 219 MET cc_start: -0.0982 (OUTLIER) cc_final: -0.1254 (mtt) REVERT: A 427 HIS cc_start: 0.1968 (t-90) cc_final: 0.1421 (t-90) REVERT: A 450 MET cc_start: 0.1845 (pmt) cc_final: 0.1107 (mmp) REVERT: A 1260 MET cc_start: 0.1767 (mmp) cc_final: 0.0588 (tmm) REVERT: A 1421 MET cc_start: 0.3048 (ptp) cc_final: 0.2595 (ptp) REVERT: B 80 ASN cc_start: 0.4532 (t0) cc_final: 0.3744 (m-40) REVERT: B 171 MET cc_start: -0.0910 (mtt) cc_final: -0.1302 (mtt) REVERT: B 188 ASN cc_start: 0.2643 (t0) cc_final: 0.2137 (m110) REVERT: B 224 THR cc_start: 0.4979 (m) cc_final: 0.4750 (t) REVERT: B 283 PHE cc_start: 0.2473 (t80) cc_final: 0.1755 (t80) REVERT: B 312 MET cc_start: 0.0714 (pmm) cc_final: 0.0292 (pmm) REVERT: B 403 ILE cc_start: 0.5925 (pt) cc_final: 0.5684 (tp) REVERT: B 818 ILE cc_start: -0.0601 (OUTLIER) cc_final: -0.1178 (tt) REVERT: B 885 MET cc_start: 0.2864 (tmm) cc_final: 0.2505 (pmm) REVERT: B 1077 GLN cc_start: -0.1083 (mm-40) cc_final: -0.1399 (mm-40) REVERT: C 1 MET cc_start: -0.0425 (tmm) cc_final: -0.1310 (ptt) REVERT: C 112 MET cc_start: 0.5978 (tmm) cc_final: 0.5497 (ttm) REVERT: D 29 TRP cc_start: 0.3351 (m100) cc_final: 0.3078 (m100) REVERT: E 50 MET cc_start: 0.1508 (tpt) cc_final: 0.0995 (ptt) REVERT: F 103 MET cc_start: 0.0744 (ptt) cc_final: 0.0466 (tpt) REVERT: I 1 MET cc_start: 0.1511 (mmm) cc_final: 0.0372 (ptt) REVERT: J 41 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.1374 (mp) REVERT: K 121 LEU cc_start: 0.0352 (tp) cc_final: -0.0543 (pp) REVERT: N 305 MET cc_start: 0.0710 (mpt) cc_final: -0.1019 (mtm) REVERT: N 374 LYS cc_start: 0.1831 (tptp) cc_final: 0.1517 (tttm) REVERT: O 197 MET cc_start: 0.2360 (ppp) cc_final: 0.1867 (ppp) REVERT: P 175 ILE cc_start: 0.6499 (mt) cc_final: 0.6102 (tt) REVERT: P 239 ASN cc_start: 0.4932 (p0) cc_final: 0.4553 (m110) REVERT: P 294 PHE cc_start: 0.2936 (t80) cc_final: 0.1556 (t80) outliers start: 89 outliers final: 39 residues processed: 469 average time/residue: 0.2047 time to fit residues: 159.3789 Evaluate side-chains 369 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 327 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1350 VAL Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain M residue 132 ASN Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 409 LEU Chi-restraints excluded: chain O residue 90 SER Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 572 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 54 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 456 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 352 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 408 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 469 optimal weight: 0.9990 chunk 268 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN K 95 HIS O 240 GLN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 GLN ** 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 = 0.4544 r_free = 0.4544 target = 0.227550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.196500 restraints weight = 57019.428| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.14 r_work: 0.4076 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1254 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 39032 Z= 0.132 Angle : 0.703 16.175 52693 Z= 0.359 Chirality : 0.045 0.198 5961 Planarity : 0.005 0.086 6778 Dihedral : 6.419 78.327 5230 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.61 % Favored : 88.14 % Rotamer: Outliers : 2.23 % Allowed : 10.92 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.11), residues: 4765 helix: -1.66 (0.12), residues: 1526 sheet: -1.35 (0.23), residues: 498 loop : -3.08 (0.10), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 368 TYR 0.024 0.001 TYR P 249 PHE 0.029 0.002 PHE G 140 TRP 0.015 0.001 TRP O 583 HIS 0.008 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00278 (39016) covalent geometry : angle 0.70014 (52687) hydrogen bonds : bond 0.04006 ( 1058) hydrogen bonds : angle 5.14559 ( 3045) metal coordination : bond 0.00557 ( 16) metal coordination : angle 5.74123 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 328 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TRP cc_start: 0.4858 (t60) cc_final: 0.4163 (t60) REVERT: A 273 MET cc_start: -0.0032 (ptt) cc_final: -0.1602 (mtm) REVERT: A 427 HIS cc_start: 0.1814 (t-90) cc_final: 0.1524 (t-90) REVERT: A 450 MET cc_start: 0.1950 (pmt) cc_final: 0.1215 (mmp) REVERT: A 809 MET cc_start: 0.3216 (mmp) cc_final: 0.2934 (tpp) REVERT: A 1260 MET cc_start: 0.1561 (mmp) cc_final: 0.0513 (tmm) REVERT: A 1421 MET cc_start: 0.2862 (ptp) cc_final: 0.2583 (ptm) REVERT: B 80 ASN cc_start: 0.4792 (t0) cc_final: 0.4443 (t0) REVERT: B 188 ASN cc_start: 0.3644 (t0) cc_final: 0.2524 (t0) REVERT: B 312 MET cc_start: 0.1060 (pmm) cc_final: 0.0518 (pmm) REVERT: B 317 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3761 (pt) REVERT: B 358 MET cc_start: -0.1701 (mmp) cc_final: -0.2438 (ptp) REVERT: B 818 ILE cc_start: -0.0656 (pt) cc_final: -0.1069 (tt) REVERT: B 944 MET cc_start: -0.1134 (pmm) cc_final: -0.2204 (ppp) REVERT: B 945 ASN cc_start: 0.2925 (p0) cc_final: 0.2480 (p0) REVERT: C 1 MET cc_start: -0.0220 (tmm) cc_final: -0.1865 (ptt) REVERT: C 313 ILE cc_start: 0.2624 (OUTLIER) cc_final: 0.2118 (mt) REVERT: E 50 MET cc_start: 0.1639 (tpt) cc_final: 0.1011 (ptt) REVERT: F 103 MET cc_start: 0.0624 (ptt) cc_final: 0.0361 (tpt) REVERT: I 1 MET cc_start: 0.1426 (mmm) cc_final: 0.0410 (ptt) REVERT: L 28 LYS cc_start: 0.3688 (pttp) cc_final: 0.2807 (pttp) REVERT: N 305 MET cc_start: 0.0792 (mpt) cc_final: -0.1100 (mtm) REVERT: O 197 MET cc_start: 0.2568 (ppp) cc_final: 0.1837 (ppp) REVERT: P 175 ILE cc_start: 0.6416 (mt) cc_final: 0.6025 (tt) REVERT: P 239 ASN cc_start: 0.4862 (p0) cc_final: 0.4527 (m-40) REVERT: P 294 PHE cc_start: 0.3182 (t80) cc_final: 0.1768 (t80) REVERT: P 300 PHE cc_start: 0.5228 (p90) cc_final: 0.4533 (p90) outliers start: 95 outliers final: 50 residues processed: 404 average time/residue: 0.1940 time to fit residues: 132.4318 Evaluate side-chains 349 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1362 MET Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 496 ILE Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain Q residue 39 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 70 optimal weight: 5.9990 chunk 325 optimal weight: 0.0670 chunk 270 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 311 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 808 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN A1142 ASN ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN M 254 GLN O 152 HIS O 298 ASN O 469 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.237375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.208317 restraints weight = 59999.000| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.46 r_work: 0.4218 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2212 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 39032 Z= 0.205 Angle : 0.840 18.962 52693 Z= 0.433 Chirality : 0.050 0.511 5961 Planarity : 0.007 0.162 6778 Dihedral : 6.624 75.406 5230 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.99 % Favored : 86.78 % Rotamer: Outliers : 3.33 % Allowed : 11.72 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.33 (0.11), residues: 4765 helix: -1.40 (0.12), residues: 1536 sheet: -1.29 (0.22), residues: 524 loop : -3.03 (0.11), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 869 TYR 0.037 0.002 TYR B1073 PHE 0.027 0.002 PHE M 162 TRP 0.044 0.003 TRP E 79 HIS 0.013 0.002 HIS P 305 Details of bonding type rmsd covalent geometry : bond 0.00442 (39016) covalent geometry : angle 0.83838 (52687) hydrogen bonds : bond 0.04320 ( 1058) hydrogen bonds : angle 5.50638 ( 3045) metal coordination : bond 0.00682 ( 16) metal coordination : angle 4.30834 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 427 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TRP cc_start: 0.4871 (t60) cc_final: 0.4157 (t60) REVERT: A 205 LEU cc_start: 0.2760 (OUTLIER) cc_final: 0.2000 (tp) REVERT: A 273 MET cc_start: -0.0515 (ptt) cc_final: -0.1744 (mtm) REVERT: A 274 MET cc_start: -0.0734 (ptt) cc_final: -0.0947 (ptp) REVERT: A 450 MET cc_start: 0.2977 (pmt) cc_final: 0.2009 (mmp) REVERT: A 454 LYS cc_start: 0.2488 (OUTLIER) cc_final: 0.1201 (mmtm) REVERT: A 945 ILE cc_start: -0.0341 (tt) cc_final: -0.1610 (pt) REVERT: A 1223 ASN cc_start: 0.3124 (p0) cc_final: 0.2920 (p0) REVERT: A 1260 MET cc_start: 0.1766 (mmp) cc_final: 0.0749 (tmm) REVERT: A 1421 MET cc_start: 0.3903 (ptp) cc_final: 0.3558 (ptp) REVERT: B 335 LEU cc_start: 0.1722 (OUTLIER) cc_final: 0.1232 (mp) REVERT: B 336 THR cc_start: 0.0925 (OUTLIER) cc_final: 0.0134 (p) REVERT: B 727 LEU cc_start: 0.2896 (mt) cc_final: 0.2487 (mp) REVERT: B 765 TYR cc_start: 0.2375 (m-10) cc_final: 0.1616 (m-80) REVERT: B 945 ASN cc_start: 0.2814 (p0) cc_final: 0.2565 (p0) REVERT: C 313 ILE cc_start: 0.2588 (OUTLIER) cc_final: 0.2368 (mt) REVERT: E 50 MET cc_start: 0.1592 (tpt) cc_final: 0.0945 (ptt) REVERT: F 103 MET cc_start: 0.0780 (ptt) cc_final: 0.0549 (tpt) REVERT: G 144 GLU cc_start: 0.5315 (pp20) cc_final: 0.3849 (pt0) REVERT: I 1 MET cc_start: 0.1422 (mmm) cc_final: 0.0458 (ptt) REVERT: I 12 LEU cc_start: 0.2173 (OUTLIER) cc_final: 0.1231 (pp) REVERT: K 81 MET cc_start: 0.2161 (tpp) cc_final: 0.1723 (tmm) REVERT: L 28 LYS cc_start: 0.4503 (pttp) cc_final: 0.3608 (pttp) REVERT: N 305 MET cc_start: 0.0624 (mpt) cc_final: -0.1447 (mtm) REVERT: O 100 GLN cc_start: 0.4115 (tp40) cc_final: 0.3820 (mm-40) REVERT: O 589 LEU cc_start: 0.1120 (OUTLIER) cc_final: 0.0833 (mp) REVERT: O 629 MET cc_start: 0.6214 (mtp) cc_final: 0.5966 (mtp) REVERT: P 175 ILE cc_start: 0.6719 (mt) cc_final: 0.6431 (tt) REVERT: P 239 ASN cc_start: 0.5011 (p0) cc_final: 0.4677 (m110) REVERT: P 294 PHE cc_start: 0.2692 (t80) cc_final: 0.1894 (t80) outliers start: 142 outliers final: 70 residues processed: 534 average time/residue: 0.2097 time to fit residues: 187.2360 Evaluate side-chains 411 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 334 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 293 SER Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 622 SER Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain Q residue 39 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 346 optimal weight: 5.9990 chunk 160 optimal weight: 0.3980 chunk 256 optimal weight: 2.9990 chunk 211 optimal weight: 0.4980 chunk 306 optimal weight: 10.0000 chunk 466 optimal weight: 0.3980 chunk 286 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 465 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 134 ASN A 156 HIS A 233 GLN A 311 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN B 840 GLN ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN C 14 ASN C 88 ASN C 99 HIS C 158 ASN E 99 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 572 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.239322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.212139 restraints weight = 60710.892| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 2.45 r_work: 0.4273 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2500 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 39032 Z= 0.154 Angle : 0.724 15.850 52693 Z= 0.372 Chirality : 0.046 0.281 5961 Planarity : 0.005 0.096 6778 Dihedral : 6.245 74.817 5227 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.02 % Favored : 88.75 % Rotamer: Outliers : 2.51 % Allowed : 13.69 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.11), residues: 4765 helix: -1.05 (0.13), residues: 1528 sheet: -1.22 (0.23), residues: 508 loop : -2.84 (0.11), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 60 TYR 0.023 0.002 TYR P 249 PHE 0.044 0.002 PHE B 718 TRP 0.024 0.001 TRP O 583 HIS 0.013 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00330 (39016) covalent geometry : angle 0.72300 (52687) hydrogen bonds : bond 0.03695 ( 1058) hydrogen bonds : angle 5.13388 ( 3045) metal coordination : bond 0.00650 ( 16) metal coordination : angle 3.46458 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 380 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.2902 (pmt) cc_final: 0.2010 (mmp) REVERT: A 945 ILE cc_start: 0.0055 (tt) cc_final: -0.1343 (pt) REVERT: A 1260 MET cc_start: 0.1236 (mmp) cc_final: 0.0307 (tmm) REVERT: A 1348 MET cc_start: 0.0367 (tpt) cc_final: -0.0188 (ttt) REVERT: A 1421 MET cc_start: 0.4403 (ptp) cc_final: 0.3809 (ptp) REVERT: B 335 LEU cc_start: 0.2012 (OUTLIER) cc_final: 0.1774 (mp) REVERT: B 360 MET cc_start: 0.4475 (mmt) cc_final: 0.3174 (mmt) REVERT: B 439 THR cc_start: 0.5143 (m) cc_final: 0.3646 (t) REVERT: B 765 TYR cc_start: 0.3166 (m-10) cc_final: 0.2583 (m-80) REVERT: B 931 MET cc_start: 0.3261 (OUTLIER) cc_final: 0.1788 (mtt) REVERT: B 1101 MET cc_start: 0.7170 (ttp) cc_final: 0.6875 (ptp) REVERT: C 1 MET cc_start: 0.0029 (tmm) cc_final: -0.1285 (ptt) REVERT: C 201 GLU cc_start: 0.4487 (tm-30) cc_final: 0.3925 (tt0) REVERT: E 50 MET cc_start: 0.1649 (tpt) cc_final: 0.0996 (ptt) REVERT: E 149 LEU cc_start: 0.2377 (tp) cc_final: 0.1499 (pt) REVERT: G 144 GLU cc_start: 0.5557 (pp20) cc_final: 0.4391 (pt0) REVERT: I 1 MET cc_start: 0.1166 (mmm) cc_final: 0.0186 (ptt) REVERT: I 12 LEU cc_start: 0.2117 (OUTLIER) cc_final: 0.0924 (pp) REVERT: K 81 MET cc_start: 0.2687 (tpp) cc_final: 0.2020 (tmm) REVERT: N 305 MET cc_start: 0.1193 (mpt) cc_final: -0.0765 (mtm) REVERT: O 206 LEU cc_start: 0.2501 (OUTLIER) cc_final: 0.2268 (mm) REVERT: O 577 MET cc_start: 0.6510 (tpp) cc_final: 0.6236 (tpp) REVERT: P 175 ILE cc_start: 0.6780 (mt) cc_final: 0.6407 (tt) outliers start: 107 outliers final: 57 residues processed: 462 average time/residue: 0.1893 time to fit residues: 149.9897 Evaluate side-chains 381 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 622 SER Chi-restraints excluded: chain O residue 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 276 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 307 optimal weight: 0.0050 chunk 204 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 392 optimal weight: 0.7980 chunk 362 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 134 optimal weight: 0.2980 chunk 268 optimal weight: 0.4980 chunk 430 optimal weight: 0.0970 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 434 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS O 572 HIS O 579 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.240218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.213282 restraints weight = 61094.889| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.47 r_work: 0.4291 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2582 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 39032 Z= 0.115 Angle : 0.672 11.911 52693 Z= 0.343 Chirality : 0.044 0.189 5961 Planarity : 0.005 0.082 6778 Dihedral : 5.990 74.751 5227 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.71 % Favored : 88.10 % Rotamer: Outliers : 2.30 % Allowed : 14.44 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.12), residues: 4765 helix: -0.76 (0.13), residues: 1536 sheet: -0.99 (0.23), residues: 504 loop : -2.76 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 973 TYR 0.023 0.001 TYR B 241 PHE 0.022 0.001 PHE O 249 TRP 0.020 0.001 TRP O 583 HIS 0.026 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00238 (39016) covalent geometry : angle 0.67065 (52687) hydrogen bonds : bond 0.03311 ( 1058) hydrogen bonds : angle 4.91861 ( 3045) metal coordination : bond 0.00352 ( 16) metal coordination : angle 3.39737 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.2739 (OUTLIER) cc_final: 0.2015 (tp) REVERT: A 450 MET cc_start: 0.2987 (pmt) cc_final: 0.2103 (mmp) REVERT: A 473 LEU cc_start: 0.3368 (OUTLIER) cc_final: 0.2290 (mp) REVERT: A 926 MET cc_start: 0.2398 (mmm) cc_final: 0.1861 (mmm) REVERT: A 1260 MET cc_start: 0.1060 (mmp) cc_final: 0.0092 (tmm) REVERT: A 1348 MET cc_start: 0.0477 (tpt) cc_final: -0.0033 (ttt) REVERT: A 1421 MET cc_start: 0.4762 (ptp) cc_final: 0.4176 (ptp) REVERT: B 439 THR cc_start: 0.5221 (m) cc_final: 0.4916 (p) REVERT: B 760 MET cc_start: 0.2587 (OUTLIER) cc_final: -0.1792 (ttt) REVERT: B 765 TYR cc_start: 0.3271 (OUTLIER) cc_final: 0.2732 (m-80) REVERT: B 1101 MET cc_start: 0.7527 (ttp) cc_final: 0.7169 (ptp) REVERT: C 1 MET cc_start: 0.0237 (tmm) cc_final: -0.1436 (ptt) REVERT: E 50 MET cc_start: 0.1664 (tpt) cc_final: 0.1018 (ptt) REVERT: E 121 MET cc_start: 0.4743 (ttm) cc_final: 0.4537 (ttp) REVERT: E 149 LEU cc_start: 0.2244 (tp) cc_final: 0.1257 (pt) REVERT: E 215 MET cc_start: 0.3084 (mmp) cc_final: 0.2810 (mmp) REVERT: F 103 MET cc_start: 0.2293 (tpt) cc_final: 0.1599 (tpp) REVERT: G 144 GLU cc_start: 0.5391 (pp20) cc_final: 0.4280 (pt0) REVERT: I 1 MET cc_start: 0.1269 (mmm) cc_final: 0.0228 (ptt) REVERT: I 12 LEU cc_start: 0.2125 (OUTLIER) cc_final: 0.0963 (pp) REVERT: J 2 ILE cc_start: 0.1124 (OUTLIER) cc_final: 0.0299 (mt) REVERT: K 81 MET cc_start: 0.2616 (tpp) cc_final: 0.2049 (tmm) REVERT: M 118 LEU cc_start: 0.5974 (mt) cc_final: 0.5600 (mp) REVERT: N 305 MET cc_start: 0.1170 (mpt) cc_final: -0.0805 (mtm) REVERT: O 206 LEU cc_start: 0.2402 (OUTLIER) cc_final: 0.2160 (mm) REVERT: O 320 GLU cc_start: 0.4950 (mm-30) cc_final: 0.4685 (tt0) REVERT: O 629 MET cc_start: 0.6153 (mtp) cc_final: 0.5746 (ttm) REVERT: P 175 ILE cc_start: 0.6641 (mt) cc_final: 0.6287 (tt) REVERT: P 184 ARG cc_start: 0.7282 (ttm110) cc_final: 0.6956 (mtp85) outliers start: 98 outliers final: 69 residues processed: 434 average time/residue: 0.2045 time to fit residues: 153.4006 Evaluate side-chains 404 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 328 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 928 GLN Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 1027 LEU Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 311 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 207 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 434 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 381 optimal weight: 10.0000 chunk 257 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 358 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 805 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1218 GLN ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN B 374 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN B 928 GLN ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS M 89 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN N 289 HIS N 377 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 GLN O 298 ASN O 579 GLN O 584 ASN O 599 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.250298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.228463 restraints weight = 64334.126| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 1.98 r_work: 0.4426 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4602 moved from start: 1.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.221 39032 Z= 0.325 Angle : 1.123 19.912 52693 Z= 0.582 Chirality : 0.059 0.407 5961 Planarity : 0.009 0.121 6778 Dihedral : 7.542 74.464 5227 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.34 % Favored : 84.41 % Rotamer: Outliers : 3.40 % Allowed : 14.65 % Favored : 81.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.11), residues: 4765 helix: -1.58 (0.12), residues: 1473 sheet: -1.43 (0.23), residues: 461 loop : -3.14 (0.10), residues: 2831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A 153 TYR 0.040 0.004 TYR H 95 PHE 0.059 0.004 PHE H 10 TRP 0.051 0.004 TRP O 583 HIS 0.047 0.004 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00741 (39016) covalent geometry : angle 1.12043 (52687) hydrogen bonds : bond 0.05658 ( 1058) hydrogen bonds : angle 6.46785 ( 3045) metal coordination : bond 0.01895 ( 16) metal coordination : angle 6.73146 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 559 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: -0.0437 (ptt) cc_final: -0.1931 (mtm) REVERT: A 379 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 648 ASN cc_start: 0.3617 (p0) cc_final: 0.3174 (t0) REVERT: A 809 MET cc_start: 0.4690 (mmp) cc_final: 0.3504 (mmt) REVERT: A 1260 MET cc_start: 0.1774 (mmp) cc_final: 0.0355 (tmm) REVERT: A 1348 MET cc_start: 0.0139 (tpt) cc_final: -0.0190 (ttt) REVERT: B 312 MET cc_start: 0.2765 (pmm) cc_final: 0.1759 (mtm) REVERT: B 631 LEU cc_start: 0.3678 (OUTLIER) cc_final: 0.3426 (mm) REVERT: B 705 MET cc_start: 0.2321 (OUTLIER) cc_final: 0.1853 (tpp) REVERT: B 765 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6339 (m-10) REVERT: C 1 MET cc_start: 0.0240 (tmm) cc_final: -0.1161 (ptt) REVERT: C 71 MET cc_start: 0.6098 (tpp) cc_final: 0.5891 (tpp) REVERT: C 97 LEU cc_start: 0.1462 (OUTLIER) cc_final: 0.1152 (tt) REVERT: C 202 ILE cc_start: 0.8717 (mt) cc_final: 0.8188 (mt) REVERT: C 322 LYS cc_start: 0.6065 (tttm) cc_final: 0.5277 (ttmt) REVERT: E 50 MET cc_start: 0.1778 (tpt) cc_final: 0.0915 (ptt) REVERT: F 112 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5895 (tt0) REVERT: I 1 MET cc_start: 0.1526 (mmm) cc_final: 0.0298 (ptt) REVERT: I 12 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1371 (pp) REVERT: K 125 MET cc_start: 0.3610 (mmm) cc_final: 0.3116 (tpp) REVERT: M 119 TRP cc_start: 0.3427 (OUTLIER) cc_final: 0.2424 (m100) REVERT: N 398 SER cc_start: 0.5224 (m) cc_final: 0.4709 (t) REVERT: O 52 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6364 (mt) REVERT: O 197 MET cc_start: 0.3129 (OUTLIER) cc_final: 0.2439 (ppp) REVERT: O 296 LEU cc_start: 0.7253 (mt) cc_final: 0.6958 (mm) REVERT: O 516 LEU cc_start: 0.1748 (OUTLIER) cc_final: 0.1538 (tp) REVERT: O 629 MET cc_start: 0.7249 (mtp) cc_final: 0.6905 (ttm) REVERT: P 294 PHE cc_start: 0.4004 (t80) cc_final: 0.2709 (t80) REVERT: P 311 TYR cc_start: 0.3330 (OUTLIER) cc_final: 0.1896 (m-80) outliers start: 145 outliers final: 66 residues processed: 661 average time/residue: 0.2135 time to fit residues: 233.9635 Evaluate side-chains 486 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 409 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 345 PHE Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 622 SER Chi-restraints excluded: chain P residue 311 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 330 optimal weight: 0.6980 chunk 304 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 358 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 247 optimal weight: 0.0000 chunk 67 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 386 ASN ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN B 116 HIS B 237 ASN B 299 GLN B 456 HIS ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 883 GLN B 936 GLN ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN C 207 HIS D 8 ASN D 133 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN K 95 HIS ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN N 284 ASN O 298 ASN O 652 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.251903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.231122 restraints weight = 64116.150| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 1.93 r_work: 0.4426 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4600 moved from start: 1.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 39032 Z= 0.155 Angle : 0.777 11.803 52693 Z= 0.397 Chirality : 0.047 0.234 5961 Planarity : 0.005 0.093 6778 Dihedral : 6.500 72.189 5227 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.58 % Favored : 88.18 % Rotamer: Outliers : 1.90 % Allowed : 17.46 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.11), residues: 4765 helix: -1.06 (0.13), residues: 1516 sheet: -1.22 (0.24), residues: 448 loop : -2.96 (0.10), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 482 TYR 0.024 0.002 TYR B 241 PHE 0.024 0.002 PHE O 249 TRP 0.025 0.002 TRP O 583 HIS 0.010 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00327 (39016) covalent geometry : angle 0.77545 (52687) hydrogen bonds : bond 0.03871 ( 1058) hydrogen bonds : angle 5.48933 ( 3045) metal coordination : bond 0.00667 ( 16) metal coordination : angle 5.06039 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 468 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7088 (ptp) REVERT: A 809 MET cc_start: 0.4885 (mmp) cc_final: 0.1956 (ptp) REVERT: A 890 MET cc_start: 0.6655 (tmm) cc_final: 0.5937 (tpp) REVERT: A 1117 MET cc_start: 0.5541 (tpp) cc_final: 0.5165 (tpp) REVERT: A 1260 MET cc_start: 0.1779 (mmp) cc_final: 0.0147 (tmm) REVERT: B 312 MET cc_start: 0.2309 (pmm) cc_final: 0.1553 (mtm) REVERT: B 358 MET cc_start: -0.0037 (mmp) cc_final: -0.1332 (ptp) REVERT: B 376 ARG cc_start: 0.6445 (mtt90) cc_final: 0.6189 (mtp180) REVERT: B 631 LEU cc_start: 0.3783 (OUTLIER) cc_final: 0.3486 (mm) REVERT: B 760 MET cc_start: 0.3269 (OUTLIER) cc_final: 0.0214 (ptt) REVERT: B 827 ASP cc_start: 0.7147 (p0) cc_final: 0.6752 (p0) REVERT: C 1 MET cc_start: 0.0031 (tmm) cc_final: -0.1014 (ptt) REVERT: C 71 MET cc_start: 0.5817 (tpp) cc_final: 0.5479 (tpp) REVERT: E 50 MET cc_start: 0.1477 (tpt) cc_final: 0.0969 (ptt) REVERT: I 1 MET cc_start: 0.1393 (mmm) cc_final: 0.0366 (ptt) REVERT: I 11 MET cc_start: 0.3918 (ptt) cc_final: 0.2639 (tpt) REVERT: I 12 LEU cc_start: 0.2221 (OUTLIER) cc_final: 0.1086 (pp) REVERT: J 49 MET cc_start: 0.6403 (tpt) cc_final: 0.6057 (tpt) REVERT: K 81 MET cc_start: 0.3861 (tpp) cc_final: 0.2079 (tmm) REVERT: K 125 MET cc_start: 0.4292 (mmm) cc_final: 0.3092 (tpp) REVERT: L 28 LYS cc_start: 0.6139 (pttt) cc_final: 0.5846 (pttt) REVERT: N 398 SER cc_start: 0.5015 (m) cc_final: 0.4537 (t) REVERT: O 296 LEU cc_start: 0.7017 (mt) cc_final: 0.6764 (mm) REVERT: P 184 ARG cc_start: 0.7371 (mtp85) cc_final: 0.7158 (mtp85) REVERT: P 185 PHE cc_start: 0.6416 (t80) cc_final: 0.5497 (t80) REVERT: P 294 PHE cc_start: 0.3622 (t80) cc_final: 0.2312 (t80) REVERT: P 311 TYR cc_start: 0.3599 (OUTLIER) cc_final: 0.2230 (m-80) outliers start: 81 outliers final: 55 residues processed: 529 average time/residue: 0.2276 time to fit residues: 203.5462 Evaluate side-chains 458 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 398 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 311 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 117 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 465 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 363 optimal weight: 0.0040 chunk 11 optimal weight: 0.9980 chunk 407 optimal weight: 0.1980 chunk 335 optimal weight: 8.9990 chunk 425 optimal weight: 1.9990 chunk 470 optimal weight: 0.0470 chunk 183 optimal weight: 0.9980 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.252074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.230461 restraints weight = 64128.401| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 1.89 r_work: 0.4429 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4649 moved from start: 1.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39032 Z= 0.127 Angle : 0.734 13.800 52693 Z= 0.371 Chirality : 0.046 0.262 5961 Planarity : 0.005 0.073 6778 Dihedral : 6.110 72.623 5227 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.73 % Favored : 88.04 % Rotamer: Outliers : 1.88 % Allowed : 17.84 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.11), residues: 4765 helix: -0.66 (0.13), residues: 1513 sheet: -1.15 (0.23), residues: 471 loop : -2.82 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 499 TYR 0.026 0.001 TYR E 46 PHE 0.031 0.001 PHE O 249 TRP 0.027 0.002 TRP A 316 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00272 (39016) covalent geometry : angle 0.73323 (52687) hydrogen bonds : bond 0.03399 ( 1058) hydrogen bonds : angle 5.15821 ( 3045) metal coordination : bond 0.00490 ( 16) metal coordination : angle 3.79020 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 418 time to evaluate : 1.473 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 274 MET cc_start: -0.0831 (ptt) cc_final: -0.1088 (ptp) REVERT: A 802 SER cc_start: 0.5942 (p) cc_final: 0.5358 (m) REVERT: A 809 MET cc_start: 0.4833 (mmp) cc_final: 0.1942 (ptp) REVERT: A 890 MET cc_start: 0.6561 (tmm) cc_final: 0.5889 (tpp) REVERT: A 1117 MET cc_start: 0.5676 (tpp) cc_final: 0.5275 (tpp) REVERT: A 1260 MET cc_start: 0.1744 (mmp) cc_final: 0.0253 (tmm) REVERT: B 312 MET cc_start: 0.2183 (pmm) cc_final: 0.1404 (mtm) REVERT: B 358 MET cc_start: 0.0088 (mmp) cc_final: -0.1074 (ptp) REVERT: B 376 ARG cc_start: 0.6522 (mtt90) cc_final: 0.6272 (mtp180) REVERT: B 435 ARG cc_start: 0.7179 (mtp180) cc_final: 0.6904 (ttp-110) REVERT: B 631 LEU cc_start: 0.3734 (OUTLIER) cc_final: 0.3487 (mm) REVERT: B 760 MET cc_start: 0.3074 (tpt) cc_final: 0.0754 (ptt) REVERT: C 1 MET cc_start: 0.0129 (tmm) cc_final: -0.1371 (ptp) REVERT: C 71 MET cc_start: 0.5864 (tpp) cc_final: 0.5504 (tpp) REVERT: E 1 MET cc_start: 0.0484 (mmm) cc_final: -0.1008 (pmm) REVERT: E 39 LEU cc_start: 0.0624 (OUTLIER) cc_final: 0.0102 (mt) REVERT: E 50 MET cc_start: 0.1421 (tpt) cc_final: 0.0934 (ptm) REVERT: E 169 ARG cc_start: 0.3636 (tpt90) cc_final: 0.2867 (tpt90) REVERT: E 215 MET cc_start: 0.3804 (mmp) cc_final: 0.2589 (mtm) REVERT: F 102 SER cc_start: 0.7579 (p) cc_final: 0.7051 (m) REVERT: G 109 PHE cc_start: 0.3917 (t80) cc_final: 0.3477 (t80) REVERT: I 1 MET cc_start: 0.1583 (mmm) cc_final: 0.0496 (ptt) REVERT: I 11 MET cc_start: 0.4083 (ptt) cc_final: 0.2558 (tpt) REVERT: I 12 LEU cc_start: 0.2107 (OUTLIER) cc_final: 0.1024 (pp) REVERT: J 2 ILE cc_start: 0.4747 (OUTLIER) cc_final: 0.4446 (mt) REVERT: J 49 MET cc_start: 0.6926 (tpt) cc_final: 0.6615 (tpt) REVERT: K 81 MET cc_start: 0.3553 (tpp) cc_final: 0.1896 (tmm) REVERT: N 398 SER cc_start: 0.5071 (m) cc_final: 0.4611 (t) REVERT: O 296 LEU cc_start: 0.7063 (mt) cc_final: 0.6829 (mm) REVERT: P 185 PHE cc_start: 0.6317 (t80) cc_final: 0.5505 (t80) REVERT: P 294 PHE cc_start: 0.3125 (t80) cc_final: 0.2079 (t80) REVERT: P 311 TYR cc_start: 0.3524 (OUTLIER) cc_final: 0.2273 (m-80) outliers start: 80 outliers final: 51 residues processed: 478 average time/residue: 0.2132 time to fit residues: 173.4264 Evaluate side-chains 447 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 391 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 589 HIS Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 311 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 408 optimal weight: 0.9990 chunk 455 optimal weight: 0.8980 chunk 326 optimal weight: 0.7980 chunk 306 optimal weight: 4.9990 chunk 456 optimal weight: 1.9990 chunk 374 optimal weight: 3.9990 chunk 466 optimal weight: 0.0370 chunk 288 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 chunk 220 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN A 913 GLN A1103 GLN A1346 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 133 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN O 579 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.250547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.227043 restraints weight = 63288.332| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 2.18 r_work: 0.4370 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4997 moved from start: 1.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.292 39032 Z= 0.154 Angle : 0.757 14.547 52693 Z= 0.385 Chirality : 0.047 0.421 5961 Planarity : 0.005 0.095 6778 Dihedral : 6.060 74.329 5227 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.77 % Favored : 88.00 % Rotamer: Outliers : 1.62 % Allowed : 18.38 % Favored : 80.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.11), residues: 4765 helix: -0.56 (0.13), residues: 1521 sheet: -1.13 (0.22), residues: 510 loop : -2.79 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 607 TYR 0.024 0.002 TYR B 241 PHE 0.084 0.002 PHE H 118 TRP 0.045 0.002 TRP B 442 HIS 0.011 0.001 HIS A1346 Details of bonding type rmsd covalent geometry : bond 0.00357 (39016) covalent geometry : angle 0.75569 (52687) hydrogen bonds : bond 0.03477 ( 1058) hydrogen bonds : angle 5.11096 ( 3045) metal coordination : bond 0.00513 ( 16) metal coordination : angle 3.85387 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 452 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ASN cc_start: 0.4698 (t0) cc_final: 0.4312 (t0) REVERT: A 802 SER cc_start: 0.6522 (p) cc_final: 0.5975 (m) REVERT: A 809 MET cc_start: 0.5044 (mmp) cc_final: 0.4769 (mmp) REVERT: A 890 MET cc_start: 0.6692 (tmm) cc_final: 0.6091 (tpp) REVERT: A 1117 MET cc_start: 0.5651 (tpp) cc_final: 0.5240 (tpp) REVERT: A 1260 MET cc_start: 0.2068 (mmp) cc_final: 0.0741 (ppp) REVERT: A 1379 MET cc_start: 0.1475 (ttp) cc_final: 0.1060 (ttp) REVERT: A 1395 HIS cc_start: 0.4764 (m90) cc_final: 0.4549 (m-70) REVERT: B 312 MET cc_start: 0.2252 (pmm) cc_final: 0.1482 (mtm) REVERT: B 358 MET cc_start: 0.0243 (mmp) cc_final: -0.0750 (ptp) REVERT: B 376 ARG cc_start: 0.6742 (mtt90) cc_final: 0.6392 (mtp180) REVERT: B 760 MET cc_start: 0.3675 (tpt) cc_final: 0.1638 (ptt) REVERT: C 1 MET cc_start: 0.0494 (tmm) cc_final: -0.1231 (ptt) REVERT: C 71 MET cc_start: 0.6677 (tpp) cc_final: 0.6427 (tpp) REVERT: C 111 ASP cc_start: 0.7392 (p0) cc_final: 0.7043 (p0) REVERT: D 120 LYS cc_start: 0.3425 (tttt) cc_final: 0.2785 (mtpt) REVERT: E 1 MET cc_start: 0.0365 (mmm) cc_final: -0.0849 (pmm) REVERT: E 39 LEU cc_start: 0.0492 (OUTLIER) cc_final: -0.0167 (mt) REVERT: E 50 MET cc_start: 0.1361 (tpt) cc_final: 0.0828 (ptm) REVERT: E 169 ARG cc_start: 0.3935 (tpt90) cc_final: 0.3192 (tpt90) REVERT: G 109 PHE cc_start: 0.4384 (t80) cc_final: 0.3678 (t80) REVERT: I 1 MET cc_start: 0.1730 (mmm) cc_final: 0.0602 (ptt) REVERT: I 11 MET cc_start: 0.4030 (ptt) cc_final: 0.2594 (tpt) REVERT: I 12 LEU cc_start: 0.1789 (OUTLIER) cc_final: 0.0987 (pp) REVERT: J 49 MET cc_start: 0.7518 (tpt) cc_final: 0.7249 (tpt) REVERT: K 81 MET cc_start: 0.3813 (tpp) cc_final: 0.1862 (tmm) REVERT: N 398 SER cc_start: 0.5180 (m) cc_final: 0.4745 (t) REVERT: O 368 ARG cc_start: 0.4939 (tpm170) cc_final: 0.4649 (mmm-85) REVERT: P 311 TYR cc_start: 0.3397 (OUTLIER) cc_final: 0.2144 (m-80) outliers start: 69 outliers final: 46 residues processed: 501 average time/residue: 0.2292 time to fit residues: 193.2571 Evaluate side-chains 454 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 405 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 589 HIS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 735 TYR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 560 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 311 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 90 optimal weight: 6.9990 chunk 386 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 418 optimal weight: 2.9990 chunk 270 optimal weight: 0.5980 chunk 406 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 255 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS O 631 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.250340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.226728 restraints weight = 63187.936| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 1.92 r_work: 0.4381 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5090 moved from start: 1.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39032 Z= 0.131 Angle : 0.738 14.403 52693 Z= 0.373 Chirality : 0.046 0.239 5961 Planarity : 0.005 0.068 6778 Dihedral : 5.948 73.071 5227 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.37 % Favored : 88.44 % Rotamer: Outliers : 1.20 % Allowed : 19.10 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.12), residues: 4765 helix: -0.43 (0.13), residues: 1523 sheet: -0.96 (0.23), residues: 483 loop : -2.71 (0.11), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 192 TYR 0.023 0.001 TYR B 241 PHE 0.064 0.002 PHE H 118 TRP 0.024 0.002 TRP O 583 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00288 (39016) covalent geometry : angle 0.73743 (52687) hydrogen bonds : bond 0.03358 ( 1058) hydrogen bonds : angle 5.00076 ( 3045) metal coordination : bond 0.00516 ( 16) metal coordination : angle 3.71013 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9586.19 seconds wall clock time: 164 minutes 52.65 seconds (9892.65 seconds total)