Starting phenix.real_space_refine on Mon Sep 14 19:26:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.map" model { file = "/net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hlq_0239/09_2026/6hlq_0239.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 76 5.49 5 Mg 1 5.21 5 S 168 5.16 5 C 20445 2.51 5 N 5704 2.21 5 O 6330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.26s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32731 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1456, 11498 Classifications: {'peptide': 1456} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1396} Chain breaks: 8 Chain: "B" Number of atoms: 9279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9279 Classifications: {'peptide': 1167} Link IDs: {'PTRANS': 59, 'TRANS': 1107} Chain breaks: 3 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 452 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1747 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain breaks: 1 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 732 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 67.782 53.472 56.339 1.00 19.73 S ATOM 480 SG CYS A 65 71.584 52.050 55.947 1.00 17.69 S ATOM 535 SG CYS A 72 70.598 53.987 59.156 1.00 18.35 S ATOM 781 SG CYS A 102 68.410 103.667 45.223 1.00 38.28 S ATOM 806 SG CYS A 105 70.997 103.152 42.657 1.00 39.53 S ATOM 1597 SG CYS A 233 71.812 105.479 45.386 1.00 37.90 S ATOM 1619 SG CYS A 236 69.337 106.296 41.729 1.00 47.04 S ATOM 20107 SG CYS B1104 82.015 62.651 48.576 1.00 12.25 S ATOM 20133 SG CYS B1107 79.991 65.648 48.376 1.00 13.03 S ATOM 20280 SG CYS B1128 78.435 62.337 48.323 1.00 21.65 S ATOM 28715 SG CYS I 10 40.952 128.595 106.167 1.00 34.82 S ATOM 28737 SG CYS I 13 40.079 124.619 105.120 1.00 38.95 S ATOM 28857 SG CYS I 30 41.307 126.792 102.096 1.00 43.34 S ATOM 29187 SG CYS I 86 74.938 90.571 154.102 1.00 63.72 S ATOM 29407 SG CYS I 114 76.925 88.424 150.907 1.00 62.33 S ATOM 29550 SG CYS J 7 88.296 42.953 126.708 1.00 6.20 S ATOM 29573 SG CYS J 10 91.755 42.305 127.284 1.00 7.07 S ATOM 29853 SG CYS J 45 91.756 46.367 128.002 1.00 8.28 S ATOM 29859 SG CYS J 46 89.793 43.567 130.009 1.00 7.04 S ATOM 30874 SG CYS L 31 47.141 42.103 110.843 1.00 22.91 S ATOM 30894 SG CYS L 34 45.457 40.469 113.658 1.00 26.64 S ATOM 30998 SG CYS L 48 44.414 39.161 110.412 1.00 35.97 S ATOM 31021 SG CYS L 51 43.370 43.262 112.414 1.00 40.02 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I3002 " occ=0.75 Time building chain proxies: 6.97, per 1000 atoms: 0.21 Number of scatterers: 32731 At special positions: 0 Unit cell: (167.44, 163.28, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 168 16.00 P 76 15.00 Mg 1 11.99 O 6330 8.00 N 5704 7.00 C 20445 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: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN I3002 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 86 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 114 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " Number of angles added : 21 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7374 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 48 sheets defined 35.4% alpha, 17.9% beta 16 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.537A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.863A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.897A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.503A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.598A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.808A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 199 removed outlier: 3.637A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 228 removed outlier: 3.535A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.595A pdb=" N VAL A 266 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.841A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.518A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.530A pdb=" N ARG A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.703A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 414 through 439 removed outlier: 3.894A pdb=" N VAL A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.901A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.686A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.734A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.615A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.700A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.579A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.739A pdb=" N TYR A 759 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.513A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.665A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.934A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.767A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.592A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.615A pdb=" N ALA A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.601A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.580A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 3.628A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 3.996A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1108 removed outlier: 4.529A pdb=" N ALA A1094 " --> pdb=" O ASP A1090 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.561A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.525A pdb=" N SER A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.605A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.825A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1247 through 1253 removed outlier: 3.610A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.254A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.550A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.516A pdb=" N LEU A1324 " --> pdb=" O GLN A1320 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1454 Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 3.520A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.186A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A1516 " --> pdb=" O GLU A1513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1516' Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 4.042A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1553 removed outlier: 3.519A pdb=" N LEU A1550 " --> pdb=" O VAL A1546 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1568 removed outlier: 3.537A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 3.590A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.525A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 removed outlier: 4.171A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1643 removed outlier: 3.999A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1638 through 1643' Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.827A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.500A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.961A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.073A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.813A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.683A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.639A pdb=" N ARG B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.625A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.786A pdb=" N ILE B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.543A pdb=" N PHE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.553A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.958A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.509A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.620A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 405 through 433 removed outlier: 3.552A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.776A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.617A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 498 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.547A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 599 through 614 removed outlier: 3.618A pdb=" N ALA B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.677A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.732A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.647A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.569A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 833 through 838 removed outlier: 4.004A pdb=" N TRP B 836 " --> pdb=" O PRO B 833 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 838' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.577A pdb=" N PHE B 954 " --> pdb=" O PRO B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 4.000A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.552A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 4.162A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 3.812A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1097 removed outlier: 3.758A pdb=" N ASP B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1093 through 1097' Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.845A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.168A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.631A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 278 through 286 removed outlier: 5.960A pdb=" N GLU C 283 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU C 284 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.520A pdb=" N ARG C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.701A pdb=" N VAL D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 removed outlier: 4.217A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.590A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.567A pdb=" N LYS E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 103 removed outlier: 3.521A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.795A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.565A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.548A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.935A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.532A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.972A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.879A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.540A pdb=" N LYS K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 3.721A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 360 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 11.285A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.619A pdb=" N SER A 371 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 378 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 486 removed outlier: 3.736A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.926A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.711A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.521A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB3, first strand: chain 'A' and resid 1507 through 1508 removed outlier: 3.909A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A1542 " --> pdb=" O THR A1239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.751A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.858A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.521A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 13 through 14 removed outlier: 4.223A pdb=" N ALA B 978 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 753 " --> pdb=" O GLN B 979 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 99 through 104 removed outlier: 5.940A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 145 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN B 151 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.313A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 216 removed outlier: 5.472A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 236 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.631A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC7, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.988A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.518A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.518A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 769 through 775 removed outlier: 3.572A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.652A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1010 through 1011 Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 56 removed outlier: 9.583A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.473A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.222A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.361A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.812A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET E 215 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 135 through 139 removed outlier: 6.347A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AF2, first strand: chain 'I' and resid 95 through 99 Processing sheet with id=AF3, first strand: chain 'K' and resid 49 through 50 removed outlier: 4.483A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 2973 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 9.62 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9551 1.33 - 1.45: 5995 1.45 - 1.58: 17554 1.58 - 1.70: 147 1.70 - 1.82: 266 Bond restraints: 33513 Sorted by residual: bond pdb=" O3B G2P T3000 " pdb=" PG G2P T3000 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O2A G2P T3000 " pdb=" PA G2P T3000 " ideal model delta sigma weight residual 1.513 1.611 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O2B G2P T3000 " pdb=" PB G2P T3000 " ideal model delta sigma weight residual 1.517 1.609 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C4 G2P T3000 " pdb=" C5 G2P T3000 " ideal model delta sigma weight residual 1.384 1.470 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C3' DC T 37 " pdb=" C2' DC T 37 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 ... (remaining 33508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 44340 2.39 - 4.79: 1095 4.79 - 7.18: 139 7.18 - 9.57: 30 9.57 - 11.97: 6 Bond angle restraints: 45610 Sorted by residual: angle pdb=" N ILE A1641 " pdb=" CA ILE A1641 " pdb=" C ILE A1641 " ideal model delta sigma weight residual 112.96 107.65 5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" O4' DC T 18 " pdb=" C4' DC T 18 " pdb=" C3' DC T 18 " ideal model delta sigma weight residual 106.00 103.40 2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" C ARG L 42 " pdb=" N THR L 43 " pdb=" CA THR L 43 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 119.31 -9.50 2.21e+00 2.05e-01 1.85e+01 ... (remaining 45605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 18939 17.55 - 35.09: 886 35.09 - 52.64: 305 52.64 - 70.18: 59 70.18 - 87.73: 15 Dihedral angle restraints: 20204 sinusoidal: 8787 harmonic: 11417 Sorted by residual: dihedral pdb=" CA ASN A 863 " pdb=" C ASN A 863 " pdb=" N LEU A 864 " pdb=" CA LEU A 864 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASP B 794 " pdb=" C ASP B 794 " pdb=" N GLU B 795 " pdb=" CA GLU B 795 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU A 781 " pdb=" C LEU A 781 " pdb=" N ASP A 782 " pdb=" CA ASP A 782 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 20201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4056 0.066 - 0.133: 882 0.133 - 0.199: 123 0.199 - 0.266: 31 0.266 - 0.332: 5 Chirality restraints: 5097 Sorted by residual: chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE A 581 " pdb=" CA ILE A 581 " pdb=" CG1 ILE A 581 " pdb=" CG2 ILE A 581 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5094 not shown) Planarity restraints: 5637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO E 151 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " 0.025 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR B1033 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 836 " 0.023 2.00e-02 2.50e+03 1.69e-02 7.13e+00 pdb=" CG TRP B 836 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 836 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 836 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 836 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 836 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 836 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 836 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 836 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 836 " 0.007 2.00e-02 2.50e+03 ... (remaining 5634 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 37 2.37 - 3.01: 15208 3.01 - 3.64: 48088 3.64 - 4.27: 77846 4.27 - 4.90: 127605 Nonbonded interactions: 268784 Sorted by model distance: nonbonded pdb=" O3' C R 20 " pdb="MG MG R 101 " model vdw 1.742 2.170 nonbonded pdb=" OD1 ASP A 629 " pdb="MG MG R 101 " model vdw 1.824 2.170 nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG R 101 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR A 621 " pdb=" O ALA A 626 " model vdw 2.229 3.040 nonbonded pdb=" O VAL A 483 " pdb=" OG1 THR A 613 " model vdw 2.248 3.040 ... (remaining 268779 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=0.75 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 39.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 0.338 33537 Z= 0.330 Angle : 0.983 47.219 45631 Z= 0.508 Chirality : 0.058 0.332 5097 Planarity : 0.007 0.084 5637 Dihedral : 12.317 87.728 12830 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.10), residues: 3870 helix: -4.36 (0.06), residues: 1260 sheet: -2.36 (0.19), residues: 577 loop : -2.15 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 920 TYR 0.055 0.003 TYR B1033 PHE 0.030 0.003 PHE B 545 TRP 0.044 0.003 TRP B 836 HIS 0.014 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.28 (33513) covalent geometry : angle 0.90825 / 0.50 (45610) hydrogen bonds : bond 0.29638 / 19.50 ( 1092) hydrogen bonds : angle 10.26010 / 7.05 ( 3055) metal coordination : bond 0.20107 / 13.19 ( 24) metal coordination : angle 17.51606 / 10.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1020 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8120 (tp) cc_final: 0.7842 (tp) REVERT: A 179 ASN cc_start: 0.8031 (t0) cc_final: 0.7250 (m-40) REVERT: A 399 LEU cc_start: 0.8550 (mm) cc_final: 0.8242 (mm) REVERT: A 769 VAL cc_start: 0.9321 (m) cc_final: 0.9087 (t) REVERT: A 924 SER cc_start: 0.9143 (t) cc_final: 0.8923 (m) REVERT: A 937 ASN cc_start: 0.7462 (t0) cc_final: 0.7235 (m-40) REVERT: A 938 VAL cc_start: 0.9252 (p) cc_final: 0.8919 (t) REVERT: A 1120 TYR cc_start: 0.6880 (m-80) cc_final: 0.6407 (m-80) REVERT: A 1170 MET cc_start: 0.8824 (mmp) cc_final: 0.8482 (mmm) REVERT: A 1292 ILE cc_start: 0.8872 (mm) cc_final: 0.8551 (mt) REVERT: A 1466 SER cc_start: 0.7085 (m) cc_final: 0.6696 (m) REVERT: B 550 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7358 (mmt-90) REVERT: B 763 ASP cc_start: 0.7920 (m-30) cc_final: 0.7700 (m-30) REVERT: C 183 PRO cc_start: 0.8776 (Cg_endo) cc_final: 0.8438 (Cg_exo) REVERT: E 14 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7520 (mtm-85) REVERT: G 72 LYS cc_start: 0.8482 (mptt) cc_final: 0.8169 (mptt) REVERT: K 138 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8318 (mmmt) REVERT: L 64 LEU cc_start: 0.8839 (tp) cc_final: 0.8546 (tp) outliers start: 3 outliers final: 2 residues processed: 1022 average time/residue: 0.2322 time to fit residues: 370.0656 Evaluate side-chains 590 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 588 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 384 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 673 HIS A 863 ASN A 880 GLN A 923 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1141 GLN A1237 GLN A1244 ASN A1648 ASN B 171 HIS B 182 GLN B 224 ASN B 724 GLN B 745 GLN B1010 ASN C 32 ASN C 65 ASN C 137 ASN C 175 GLN D 17 ASN D 26 GLN D 29 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 63 GLN G 74 ASN G 161 ASN H 128 ASN K 106 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.153284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.118158 restraints weight = 37867.574| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.24 r_work: 0.3044 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33537 Z= 0.139 Angle : 0.656 13.875 45631 Z= 0.346 Chirality : 0.045 0.192 5097 Planarity : 0.005 0.058 5637 Dihedral : 13.139 87.779 5082 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.45 % Allowed : 10.34 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.12), residues: 3870 helix: -2.48 (0.11), residues: 1293 sheet: -1.97 (0.20), residues: 564 loop : -1.72 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1047 TYR 0.023 0.002 TYR A1302 PHE 0.019 0.001 PHE B 407 TRP 0.022 0.002 TRP G 125 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (33513) covalent geometry : angle 0.64811 / 0.35 (45610) hydrogen bonds : bond 0.05410 / 3.50 ( 1092) hydrogen bonds : angle 5.90379 / 4.09 ( 3055) metal coordination : bond 0.00952 / 0.61 ( 24) metal coordination : angle 4.83714 / 2.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 657 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 179 ASN cc_start: 0.7929 (t0) cc_final: 0.6875 (m-40) REVERT: A 399 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8200 (mm) REVERT: A 433 ASP cc_start: 0.7538 (m-30) cc_final: 0.7287 (m-30) REVERT: A 490 ILE cc_start: 0.8452 (mm) cc_final: 0.8237 (mm) REVERT: A 646 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 672 ASP cc_start: 0.8926 (m-30) cc_final: 0.8609 (m-30) REVERT: A 937 ASN cc_start: 0.7950 (t0) cc_final: 0.7623 (m-40) REVERT: A 1120 TYR cc_start: 0.7093 (m-80) cc_final: 0.6885 (m-10) REVERT: A 1170 MET cc_start: 0.9174 (mmp) cc_final: 0.8768 (mmp) REVERT: A 1295 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8233 (ttm170) REVERT: B 53 THR cc_start: 0.8719 (m) cc_final: 0.8510 (p) REVERT: B 397 THR cc_start: 0.9091 (t) cc_final: 0.8838 (m) REVERT: B 550 ARG cc_start: 0.8155 (ptp90) cc_final: 0.7479 (mmt180) REVERT: B 720 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8287 (tp40) REVERT: B 762 MET cc_start: 0.8885 (mmt) cc_final: 0.8541 (mmt) REVERT: B 763 ASP cc_start: 0.8575 (m-30) cc_final: 0.8350 (m-30) REVERT: B 867 ASN cc_start: 0.8189 (m-40) cc_final: 0.7807 (t0) REVERT: B 1111 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8146 (pt) REVERT: C 47 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7940 (mt) REVERT: C 183 PRO cc_start: 0.8744 (Cg_endo) cc_final: 0.8533 (Cg_exo) REVERT: D 38 GLN cc_start: 0.7422 (tt0) cc_final: 0.7147 (mt0) REVERT: E 6 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7113 (mm-30) REVERT: E 36 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8204 (mp0) REVERT: F 70 LYS cc_start: 0.8671 (tttt) cc_final: 0.8416 (tttm) REVERT: G 72 LYS cc_start: 0.8377 (mptt) cc_final: 0.8139 (mptt) REVERT: G 76 LYS cc_start: 0.7354 (tptm) cc_final: 0.7061 (tppp) REVERT: H 27 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8260 (mt-10) REVERT: H 96 VAL cc_start: 0.8836 (p) cc_final: 0.8409 (t) REVERT: I 29 GLU cc_start: 0.6492 (tp30) cc_final: 0.5964 (pt0) REVERT: I 94 MET cc_start: 0.2787 (ttm) cc_final: 0.2262 (ttt) REVERT: K 122 LYS cc_start: 0.8802 (tptt) cc_final: 0.8519 (tptp) REVERT: K 131 VAL cc_start: 0.8937 (p) cc_final: 0.8651 (t) REVERT: K 138 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7940 (mmmm) REVERT: L 64 LEU cc_start: 0.9049 (tp) cc_final: 0.8695 (tp) outliers start: 85 outliers final: 48 residues processed: 704 average time/residue: 0.2197 time to fit residues: 245.7535 Evaluate side-chains 617 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 565 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 62 optimal weight: 0.0020 chunk 303 optimal weight: 3.9990 chunk 355 optimal weight: 10.0000 chunk 363 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 535 GLN A 559 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 HIS B 224 ASN B 325 GLN B 454 ASN B 480 GLN B 600 GLN B 767 ASN B 823 GLN B 899 GLN C 248 GLN E 101 GLN E 143 ASN F 78 GLN G 56 ASN G 59 GLN G 64 GLN G 75 ASN G 140 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.144863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.110510 restraints weight = 37796.899| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.19 r_work: 0.2901 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 33537 Z= 0.249 Angle : 0.723 13.205 45631 Z= 0.374 Chirality : 0.050 0.196 5097 Planarity : 0.005 0.052 5637 Dihedral : 13.140 87.484 5082 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.15 % Allowed : 11.32 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.12), residues: 3870 helix: -1.51 (0.13), residues: 1309 sheet: -1.74 (0.20), residues: 583 loop : -1.50 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1039 TYR 0.037 0.003 TYR B1033 PHE 0.030 0.002 PHE A 637 TRP 0.025 0.002 TRP B 836 HIS 0.010 0.002 HIS B1082 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 (33513) covalent geometry : angle 0.71431 / 0.37 (45610) hydrogen bonds : bond 0.04903 / 3.23 ( 1092) hydrogen bonds : angle 5.38721 / 3.74 ( 3055) metal coordination : bond 0.00655 / 0.43 ( 24) metal coordination : angle 5.11464 / 2.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 581 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7418 (t0) cc_final: 0.7159 (t0) REVERT: A 399 LEU cc_start: 0.8430 (mm) cc_final: 0.8225 (mm) REVERT: A 433 ASP cc_start: 0.7495 (m-30) cc_final: 0.7235 (m-30) REVERT: A 535 GLN cc_start: 0.8966 (mt0) cc_final: 0.8740 (mt0) REVERT: A 1089 LEU cc_start: 0.8198 (mt) cc_final: 0.7993 (mt) REVERT: A 1120 TYR cc_start: 0.7136 (m-80) cc_final: 0.6523 (m-80) REVERT: A 1170 MET cc_start: 0.9234 (mmp) cc_final: 0.8842 (mmp) REVERT: A 1266 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8517 (m) REVERT: B 296 ASP cc_start: 0.8191 (p0) cc_final: 0.7967 (p0) REVERT: B 397 THR cc_start: 0.9180 (t) cc_final: 0.8971 (m) REVERT: B 448 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7704 (ttp80) REVERT: B 550 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7494 (mmt180) REVERT: B 720 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8363 (tp40) REVERT: B 762 MET cc_start: 0.9074 (mmt) cc_final: 0.8690 (mmt) REVERT: B 763 ASP cc_start: 0.8726 (m-30) cc_final: 0.8408 (m-30) REVERT: B 835 GLU cc_start: 0.7422 (mp0) cc_final: 0.7153 (mp0) REVERT: B 867 ASN cc_start: 0.8240 (m-40) cc_final: 0.7796 (t0) REVERT: B 1111 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8075 (pp) REVERT: C 34 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8037 (tp30) REVERT: C 47 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8233 (mt) REVERT: C 183 PRO cc_start: 0.8789 (Cg_endo) cc_final: 0.8557 (Cg_exo) REVERT: C 248 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: E 6 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7185 (mm-30) REVERT: E 90 VAL cc_start: 0.6793 (OUTLIER) cc_final: 0.6419 (p) REVERT: F 70 LYS cc_start: 0.8791 (tttt) cc_final: 0.8498 (tttm) REVERT: F 112 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7751 (mm-30) REVERT: F 152 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8028 (tp) REVERT: G 72 LYS cc_start: 0.8609 (mptt) cc_final: 0.8188 (mptt) REVERT: H 27 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8148 (mt-10) REVERT: I 29 GLU cc_start: 0.6872 (tp30) cc_final: 0.6092 (pt0) REVERT: I 60 LEU cc_start: 0.9532 (tp) cc_final: 0.9311 (tp) REVERT: I 94 MET cc_start: 0.2870 (ttm) cc_final: 0.2410 (ttt) REVERT: I 106 GLU cc_start: 0.7886 (pt0) cc_final: 0.7570 (pt0) REVERT: K 81 MET cc_start: 0.8962 (mmt) cc_final: 0.8753 (mmt) REVERT: K 122 LYS cc_start: 0.8771 (tptt) cc_final: 0.8520 (tptp) REVERT: K 131 VAL cc_start: 0.8968 (p) cc_final: 0.8673 (t) REVERT: K 138 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7964 (mmmm) outliers start: 144 outliers final: 94 residues processed: 670 average time/residue: 0.2278 time to fit residues: 242.0778 Evaluate side-chains 639 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 539 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 55 optimal weight: 0.9980 chunk 319 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 373 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN A1323 HIS B 224 ASN B 767 ASN D 38 GLN F 78 GLN ** G 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.113088 restraints weight = 37575.853| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.23 r_work: 0.2938 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33537 Z= 0.123 Angle : 0.587 10.108 45631 Z= 0.308 Chirality : 0.044 0.165 5097 Planarity : 0.004 0.050 5637 Dihedral : 12.984 87.418 5082 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.99 % Allowed : 12.70 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.13), residues: 3870 helix: -0.84 (0.14), residues: 1292 sheet: -1.60 (0.20), residues: 578 loop : -1.29 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.022 0.001 TYR A1302 PHE 0.015 0.001 PHE B1167 TRP 0.019 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (33513) covalent geometry : angle 0.58298 / 0.31 (45610) hydrogen bonds : bond 0.03793 / 2.46 ( 1092) hydrogen bonds : angle 5.05481 / 3.52 ( 3055) metal coordination : bond 0.00496 / 0.31 ( 24) metal coordination : angle 3.26610 / 1.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 574 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7453 (t0) cc_final: 0.7229 (t0) REVERT: A 399 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8115 (mm) REVERT: A 433 ASP cc_start: 0.7398 (m-30) cc_final: 0.7191 (m-30) REVERT: A 535 GLN cc_start: 0.8977 (mt0) cc_final: 0.8756 (mt0) REVERT: A 562 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8491 (tt) REVERT: A 1170 MET cc_start: 0.9225 (mmp) cc_final: 0.9011 (mmp) REVERT: A 1234 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8355 (ttmm) REVERT: A 1266 VAL cc_start: 0.8874 (p) cc_final: 0.8582 (m) REVERT: A 1444 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6492 (mmt180) REVERT: B 190 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8580 (pt) REVERT: B 296 ASP cc_start: 0.8217 (p0) cc_final: 0.7959 (p0) REVERT: B 448 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7673 (ttp80) REVERT: B 550 ARG cc_start: 0.8155 (ptp90) cc_final: 0.7552 (mmt180) REVERT: B 720 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8153 (tp40) REVERT: B 762 MET cc_start: 0.9024 (mmt) cc_final: 0.8698 (mmt) REVERT: B 763 ASP cc_start: 0.8695 (m-30) cc_final: 0.8343 (m-30) REVERT: B 835 GLU cc_start: 0.7361 (mp0) cc_final: 0.7133 (mp0) REVERT: B 867 ASN cc_start: 0.8205 (m-40) cc_final: 0.7780 (t0) REVERT: B 1111 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8006 (pp) REVERT: C 47 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8064 (mt) REVERT: C 183 PRO cc_start: 0.8749 (Cg_endo) cc_final: 0.8532 (Cg_exo) REVERT: E 6 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7094 (mm-30) REVERT: E 90 VAL cc_start: 0.6672 (t) cc_final: 0.6422 (p) REVERT: F 70 LYS cc_start: 0.8762 (tttt) cc_final: 0.8476 (tttm) REVERT: F 124 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8697 (mt-10) REVERT: G 72 LYS cc_start: 0.8555 (mptt) cc_final: 0.8161 (mptt) REVERT: H 27 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8126 (mt-10) REVERT: I 29 GLU cc_start: 0.6903 (tp30) cc_final: 0.6059 (pt0) REVERT: I 60 LEU cc_start: 0.9494 (tp) cc_final: 0.9256 (tp) REVERT: I 100 GLN cc_start: 0.9064 (tp40) cc_final: 0.8694 (tp40) REVERT: K 122 LYS cc_start: 0.8757 (tptt) cc_final: 0.8540 (tptp) REVERT: K 131 VAL cc_start: 0.8937 (p) cc_final: 0.8686 (t) REVERT: K 138 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7866 (mmmm) outliers start: 104 outliers final: 75 residues processed: 634 average time/residue: 0.2331 time to fit residues: 232.0218 Evaluate side-chains 610 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 530 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 296 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 260 GLN A 263 ASN A 380 ASN A 384 GLN A1323 HIS B 224 ASN B 433 ASN B 480 GLN B 739 ASN B 767 ASN B1094 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 78 GLN J 53 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.107805 restraints weight = 37738.152| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.19 r_work: 0.2857 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 33537 Z= 0.286 Angle : 0.714 12.656 45631 Z= 0.368 Chirality : 0.050 0.218 5097 Planarity : 0.005 0.055 5637 Dihedral : 13.051 86.969 5082 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.35 % Allowed : 12.55 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.13), residues: 3870 helix: -0.77 (0.14), residues: 1307 sheet: -1.48 (0.20), residues: 573 loop : -1.28 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.025 0.002 TYR A1302 PHE 0.027 0.002 PHE B1167 TRP 0.025 0.002 TRP B 836 HIS 0.009 0.002 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.29 (33513) covalent geometry : angle 0.70712 / 0.37 (45610) hydrogen bonds : bond 0.04385 / 2.87 ( 1092) hydrogen bonds : angle 5.13090 / 3.56 ( 3055) metal coordination : bond 0.00817 / 0.52 ( 24) metal coordination : angle 4.77751 / 2.68 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 525 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7476 (t0) cc_final: 0.7260 (t0) REVERT: A 399 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 433 ASP cc_start: 0.7513 (m-30) cc_final: 0.7267 (m-30) REVERT: A 562 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8568 (tt) REVERT: A 1170 MET cc_start: 0.9223 (mmp) cc_final: 0.8791 (mmp) REVERT: A 1266 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 1326 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 1444 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6483 (mmt180) REVERT: B 134 ARG cc_start: 0.8382 (ptt-90) cc_final: 0.8094 (ptt180) REVERT: B 190 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8729 (pt) REVERT: B 296 ASP cc_start: 0.8446 (p0) cc_final: 0.8188 (p0) REVERT: B 448 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7787 (ttp80) REVERT: B 550 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7555 (mmt180) REVERT: B 699 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8513 (mt) REVERT: B 720 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8217 (tp40) REVERT: B 762 MET cc_start: 0.9078 (mmt) cc_final: 0.8680 (mmt) REVERT: B 763 ASP cc_start: 0.8800 (m-30) cc_final: 0.8531 (m-30) REVERT: B 867 ASN cc_start: 0.8266 (m-40) cc_final: 0.7880 (t0) REVERT: B 887 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8947 (mt) REVERT: B 957 ARG cc_start: 0.9054 (mpt-90) cc_final: 0.8813 (mmt90) REVERT: B 1111 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8200 (pp) REVERT: C 47 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 183 PRO cc_start: 0.8774 (Cg_endo) cc_final: 0.8545 (Cg_exo) REVERT: E 6 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7180 (mm-30) REVERT: E 90 VAL cc_start: 0.6759 (t) cc_final: 0.6485 (p) REVERT: E 163 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7965 (mt-10) REVERT: F 70 LYS cc_start: 0.8792 (tttt) cc_final: 0.8485 (tttm) REVERT: F 152 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8111 (tp) REVERT: G 72 LYS cc_start: 0.8768 (mptt) cc_final: 0.8348 (mptt) REVERT: I 29 GLU cc_start: 0.7140 (tp30) cc_final: 0.6216 (pt0) REVERT: K 122 LYS cc_start: 0.8759 (tptt) cc_final: 0.8499 (tptp) REVERT: K 131 VAL cc_start: 0.8984 (p) cc_final: 0.8692 (t) REVERT: K 138 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7849 (mmmt) outliers start: 151 outliers final: 111 residues processed: 622 average time/residue: 0.2168 time to fit residues: 214.4500 Evaluate side-chains 622 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 502 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN A 535 GLN A 590 ASN A 939 ASN A1323 HIS B 224 ASN B 739 ASN B 767 ASN E 114 ASN E 143 ASN F 78 GLN G 74 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.143483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.109527 restraints weight = 37729.300| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.21 r_work: 0.2864 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33537 Z= 0.199 Angle : 0.637 11.418 45631 Z= 0.330 Chirality : 0.046 0.215 5097 Planarity : 0.004 0.053 5637 Dihedral : 12.998 87.216 5081 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.12 % Allowed : 13.33 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.13), residues: 3870 helix: -0.46 (0.14), residues: 1289 sheet: -1.37 (0.21), residues: 572 loop : -1.15 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 356 TYR 0.023 0.002 TYR A1302 PHE 0.022 0.002 PHE B1167 TRP 0.028 0.001 TRP B 836 HIS 0.006 0.001 HIS B 646 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (33513) covalent geometry : angle 0.63086 / 0.33 (45610) hydrogen bonds : bond 0.03961 / 2.58 ( 1092) hydrogen bonds : angle 5.02690 / 3.49 ( 3055) metal coordination : bond 0.00662 / 0.43 ( 24) metal coordination : angle 4.06424 / 2.30 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 520 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 399 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8221 (mm) REVERT: A 433 ASP cc_start: 0.7529 (m-30) cc_final: 0.7275 (m-30) REVERT: A 562 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 1126 LYS cc_start: 0.7713 (mttm) cc_final: 0.7448 (mttm) REVERT: A 1170 MET cc_start: 0.9239 (mmp) cc_final: 0.8829 (mmp) REVERT: A 1266 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8679 (m) REVERT: A 1326 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 96 SER cc_start: 0.8748 (t) cc_final: 0.8410 (p) REVERT: B 190 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8693 (pt) REVERT: B 296 ASP cc_start: 0.8443 (p0) cc_final: 0.8165 (p0) REVERT: B 373 MET cc_start: 0.8730 (tpt) cc_final: 0.8465 (tpt) REVERT: B 550 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7553 (mmt180) REVERT: B 699 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8473 (mt) REVERT: B 762 MET cc_start: 0.9053 (mmt) cc_final: 0.8710 (mmt) REVERT: B 763 ASP cc_start: 0.8858 (m-30) cc_final: 0.8546 (m-30) REVERT: B 867 ASN cc_start: 0.8225 (m-40) cc_final: 0.7871 (t0) REVERT: B 887 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8952 (mt) REVERT: B 957 ARG cc_start: 0.9015 (mpt-90) cc_final: 0.8792 (mmt90) REVERT: B 1111 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8276 (pp) REVERT: C 47 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 154 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7905 (mmtt) REVERT: C 183 PRO cc_start: 0.8768 (Cg_endo) cc_final: 0.8541 (Cg_exo) REVERT: E 6 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7206 (mm-30) REVERT: E 163 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8008 (mt-10) REVERT: F 70 LYS cc_start: 0.8774 (tttt) cc_final: 0.8469 (tttm) REVERT: F 114 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: F 124 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8757 (mt-10) REVERT: F 140 ASP cc_start: 0.8768 (t0) cc_final: 0.8292 (t0) REVERT: F 152 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8095 (tp) REVERT: G 72 LYS cc_start: 0.8737 (mptt) cc_final: 0.8225 (mptt) REVERT: G 111 THR cc_start: 0.9107 (p) cc_final: 0.8863 (p) REVERT: H 22 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8198 (mtmt) REVERT: I 29 GLU cc_start: 0.7149 (tp30) cc_final: 0.6204 (pt0) REVERT: K 122 LYS cc_start: 0.8762 (tptt) cc_final: 0.8521 (tptp) REVERT: K 131 VAL cc_start: 0.9009 (p) cc_final: 0.8721 (t) REVERT: K 138 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7794 (mmmm) outliers start: 143 outliers final: 110 residues processed: 604 average time/residue: 0.2296 time to fit residues: 220.2498 Evaluate side-chains 622 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 502 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 151 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 191 optimal weight: 0.4980 chunk 339 optimal weight: 20.0000 chunk 235 optimal weight: 0.4980 chunk 351 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A1323 HIS B 224 ASN B 480 GLN B 767 ASN F 78 GLN J 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.110148 restraints weight = 37613.162| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.22 r_work: 0.2921 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33537 Z= 0.156 Angle : 0.598 11.313 45631 Z= 0.311 Chirality : 0.045 0.234 5097 Planarity : 0.004 0.053 5637 Dihedral : 12.940 87.477 5080 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.92 % Allowed : 13.96 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.13), residues: 3870 helix: -0.19 (0.14), residues: 1287 sheet: -1.33 (0.21), residues: 574 loop : -1.04 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.022 0.002 TYR A1302 PHE 0.019 0.001 PHE B1167 TRP 0.022 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (33513) covalent geometry : angle 0.59370 / 0.31 (45610) hydrogen bonds : bond 0.03693 / 2.40 ( 1092) hydrogen bonds : angle 4.91540 / 3.41 ( 3055) metal coordination : bond 0.00534 / 0.34 ( 24) metal coordination : angle 3.57238 / 2.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 522 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 399 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 433 ASP cc_start: 0.7506 (m-30) cc_final: 0.7264 (m-30) REVERT: A 562 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 1126 LYS cc_start: 0.7768 (mttm) cc_final: 0.7493 (mttm) REVERT: A 1266 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8690 (m) REVERT: A 1326 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 96 SER cc_start: 0.8740 (t) cc_final: 0.8384 (p) REVERT: B 100 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (pp20) REVERT: B 296 ASP cc_start: 0.8335 (p0) cc_final: 0.8070 (p0) REVERT: B 373 MET cc_start: 0.8688 (tpt) cc_final: 0.8454 (tpt) REVERT: B 550 ARG cc_start: 0.8120 (ptp90) cc_final: 0.7587 (mmt180) REVERT: B 685 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 699 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 762 MET cc_start: 0.9015 (mmt) cc_final: 0.8652 (mmt) REVERT: B 763 ASP cc_start: 0.8789 (m-30) cc_final: 0.8460 (m-30) REVERT: B 867 ASN cc_start: 0.8184 (m-40) cc_final: 0.7884 (t0) REVERT: B 887 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8949 (mt) REVERT: B 1111 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8298 (pp) REVERT: C 47 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8424 (mt) REVERT: C 128 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7902 (p0) REVERT: C 183 PRO cc_start: 0.8762 (Cg_endo) cc_final: 0.8543 (Cg_exo) REVERT: E 6 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7272 (mm-30) REVERT: E 163 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7943 (mt-10) REVERT: F 70 LYS cc_start: 0.8753 (tttt) cc_final: 0.8451 (tttm) REVERT: F 124 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8621 (mt-10) REVERT: F 152 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8111 (tp) REVERT: G 72 LYS cc_start: 0.8648 (mptt) cc_final: 0.8236 (mptt) REVERT: H 22 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8168 (mtmt) REVERT: I 29 GLU cc_start: 0.7098 (tp30) cc_final: 0.6188 (pt0) REVERT: K 122 LYS cc_start: 0.8766 (tptt) cc_final: 0.8534 (tptp) REVERT: K 138 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7760 (mmmm) outliers start: 136 outliers final: 103 residues processed: 604 average time/residue: 0.2342 time to fit residues: 224.6365 Evaluate side-chains 619 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 505 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 363 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 380 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN A1323 HIS B 224 ASN B 492 ASN B 739 ASN F 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.107856 restraints weight = 37844.526| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.36 r_work: 0.2834 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 33537 Z= 0.251 Angle : 0.673 12.324 45631 Z= 0.347 Chirality : 0.048 0.238 5097 Planarity : 0.005 0.055 5637 Dihedral : 12.999 87.704 5080 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.26 % Allowed : 14.14 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 3870 helix: -0.23 (0.14), residues: 1289 sheet: -1.36 (0.21), residues: 565 loop : -1.05 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.024 0.002 TYR A1302 PHE 0.028 0.002 PHE B1167 TRP 0.030 0.002 TRP B 836 HIS 0.007 0.002 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (33513) covalent geometry : angle 0.66650 / 0.35 (45610) hydrogen bonds : bond 0.04060 / 2.65 ( 1092) hydrogen bonds : angle 4.98985 / 3.45 ( 3055) metal coordination : bond 0.00729 / 0.48 ( 24) metal coordination : angle 4.26966 / 2.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 498 time to evaluate : 1.333 Fit side-chains REVERT: A 399 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8205 (mm) REVERT: A 433 ASP cc_start: 0.7622 (m-30) cc_final: 0.7373 (m-30) REVERT: A 1126 LYS cc_start: 0.7748 (mttm) cc_final: 0.7458 (mttm) REVERT: A 1266 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8670 (m) REVERT: A 1326 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 1473 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8469 (tptt) REVERT: B 96 SER cc_start: 0.8786 (t) cc_final: 0.8443 (p) REVERT: B 296 ASP cc_start: 0.8517 (p0) cc_final: 0.8276 (p0) REVERT: B 373 MET cc_start: 0.8765 (tpt) cc_final: 0.8551 (tpt) REVERT: B 550 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7542 (mmt180) REVERT: B 699 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (mt) REVERT: B 762 MET cc_start: 0.9103 (mmt) cc_final: 0.8693 (mmt) REVERT: B 763 ASP cc_start: 0.8954 (m-30) cc_final: 0.8598 (m-30) REVERT: B 867 ASN cc_start: 0.8202 (m-40) cc_final: 0.7903 (t0) REVERT: B 887 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8956 (mt) REVERT: B 1111 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8408 (pp) REVERT: C 47 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8540 (mt) REVERT: C 128 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7976 (p0) REVERT: C 183 PRO cc_start: 0.8793 (Cg_endo) cc_final: 0.8573 (Cg_exo) REVERT: C 248 GLN cc_start: 0.8960 (tt0) cc_final: 0.8442 (tt0) REVERT: E 6 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7310 (mm-30) REVERT: E 94 LYS cc_start: 0.8267 (tppt) cc_final: 0.7403 (mtmm) REVERT: E 117 THR cc_start: 0.8190 (m) cc_final: 0.7943 (p) REVERT: E 163 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8024 (mt-10) REVERT: F 70 LYS cc_start: 0.8802 (tttt) cc_final: 0.8489 (tttm) REVERT: F 114 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: F 124 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8762 (mt-10) REVERT: F 152 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8106 (tp) REVERT: G 72 LYS cc_start: 0.8712 (mptt) cc_final: 0.8325 (mptt) REVERT: H 22 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8249 (mtmt) REVERT: I 29 GLU cc_start: 0.7211 (tp30) cc_final: 0.6226 (pt0) REVERT: K 122 LYS cc_start: 0.8759 (tptt) cc_final: 0.8511 (tptp) REVERT: K 138 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7754 (mmmm) outliers start: 148 outliers final: 116 residues processed: 592 average time/residue: 0.2197 time to fit residues: 207.4841 Evaluate side-chains 619 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 493 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1473 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 25 ARG Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 373 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 355 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 chunk 36 optimal weight: 0.0470 chunk 80 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN A1323 HIS B 224 ASN B 480 GLN B 492 ASN B1165 ASN C 216 HIS F 78 GLN J 23 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.146115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.110972 restraints weight = 37419.614| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.24 r_work: 0.2923 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 33537 Z= 0.110 Angle : 0.567 9.833 45631 Z= 0.297 Chirality : 0.043 0.195 5097 Planarity : 0.004 0.056 5637 Dihedral : 12.859 87.798 5080 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.97 % Allowed : 15.58 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3870 helix: 0.16 (0.15), residues: 1288 sheet: -1.29 (0.21), residues: 568 loop : -0.91 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 356 TYR 0.021 0.001 TYR A1114 PHE 0.015 0.001 PHE B1167 TRP 0.024 0.001 TRP B 836 HIS 0.004 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (33513) covalent geometry : angle 0.56336 / 0.30 (45610) hydrogen bonds : bond 0.03373 / 2.18 ( 1092) hydrogen bonds : angle 4.79641 / 3.33 ( 3055) metal coordination : bond 0.00450 / 0.28 ( 24) metal coordination : angle 3.05742 / 1.77 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 537 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7511 (pt) REVERT: A 399 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8153 (mm) REVERT: A 433 ASP cc_start: 0.7517 (m-30) cc_final: 0.7282 (m-30) REVERT: A 601 MET cc_start: 0.8910 (mtm) cc_final: 0.8682 (mtm) REVERT: A 1126 LYS cc_start: 0.7681 (mttm) cc_final: 0.7345 (mttm) REVERT: A 1266 VAL cc_start: 0.8952 (p) cc_final: 0.8705 (m) REVERT: A 1326 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 1453 HIS cc_start: 0.6938 (m-70) cc_final: 0.6645 (m-70) REVERT: A 1473 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8414 (tptt) REVERT: B 96 SER cc_start: 0.8678 (t) cc_final: 0.8323 (p) REVERT: B 121 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8872 (t) REVERT: B 296 ASP cc_start: 0.8367 (p0) cc_final: 0.8116 (p0) REVERT: B 419 GLU cc_start: 0.8188 (tt0) cc_final: 0.7952 (tm-30) REVERT: B 492 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.8038 (t0) REVERT: B 550 ARG cc_start: 0.8190 (ptp90) cc_final: 0.7586 (mmt180) REVERT: B 685 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8292 (t) REVERT: B 762 MET cc_start: 0.9004 (mmt) cc_final: 0.8666 (mmt) REVERT: B 763 ASP cc_start: 0.8841 (m-30) cc_final: 0.8454 (m-30) REVERT: B 867 ASN cc_start: 0.8078 (m-40) cc_final: 0.7823 (t0) REVERT: B 1006 ASN cc_start: 0.8284 (p0) cc_final: 0.7803 (t0) REVERT: B 1077 ASP cc_start: 0.8571 (p0) cc_final: 0.8137 (m-30) REVERT: B 1111 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8372 (pp) REVERT: C 47 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 128 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7847 (p0) REVERT: C 183 PRO cc_start: 0.8765 (Cg_endo) cc_final: 0.8554 (Cg_exo) REVERT: C 248 GLN cc_start: 0.8931 (tt0) cc_final: 0.8447 (tt0) REVERT: C 290 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7700 (pttt) REVERT: E 94 LYS cc_start: 0.8162 (tppt) cc_final: 0.7377 (mtmm) REVERT: E 117 THR cc_start: 0.8159 (m) cc_final: 0.7945 (p) REVERT: F 70 LYS cc_start: 0.8803 (tttt) cc_final: 0.8496 (tttm) REVERT: F 124 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8572 (mt-10) REVERT: G 72 LYS cc_start: 0.8577 (mptt) cc_final: 0.8335 (mptt) REVERT: H 25 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8197 (ttt-90) REVERT: I 29 GLU cc_start: 0.7139 (tp30) cc_final: 0.6205 (pt0) REVERT: K 122 LYS cc_start: 0.8746 (tptt) cc_final: 0.8532 (tptp) REVERT: K 138 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7694 (mmmm) outliers start: 103 outliers final: 81 residues processed: 598 average time/residue: 0.2198 time to fit residues: 209.4115 Evaluate side-chains 597 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 505 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1473 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 25 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 195 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN A1323 HIS B 224 ASN B 739 ASN B 975 HIS E 143 ASN F 78 GLN J 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.108152 restraints weight = 37679.048| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.19 r_work: 0.2882 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33537 Z= 0.228 Angle : 0.653 11.324 45631 Z= 0.336 Chirality : 0.047 0.217 5097 Planarity : 0.005 0.061 5637 Dihedral : 12.899 87.761 5080 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.02 % Allowed : 15.46 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 3870 helix: 0.04 (0.15), residues: 1291 sheet: -1.37 (0.21), residues: 570 loop : -0.95 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 634 TYR 0.024 0.002 TYR A1302 PHE 0.027 0.002 PHE B1167 TRP 0.030 0.002 TRP B 836 HIS 0.007 0.002 HIS B 646 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (33513) covalent geometry : angle 0.64714 / 0.34 (45610) hydrogen bonds : bond 0.03841 / 2.51 ( 1092) hydrogen bonds : angle 4.86940 / 3.36 ( 3055) metal coordination : bond 0.00639 / 0.42 ( 24) metal coordination : angle 3.98182 / 2.26 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 498 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 433 ASP cc_start: 0.7545 (m-30) cc_final: 0.7324 (m-30) REVERT: A 601 MET cc_start: 0.8971 (mtm) cc_final: 0.8760 (mtm) REVERT: A 1126 LYS cc_start: 0.7721 (mttm) cc_final: 0.7391 (mttm) REVERT: A 1266 VAL cc_start: 0.8957 (p) cc_final: 0.8679 (m) REVERT: A 1326 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 1473 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8476 (tptt) REVERT: B 296 ASP cc_start: 0.8486 (p0) cc_final: 0.8261 (p0) REVERT: B 550 ARG cc_start: 0.8169 (ptp90) cc_final: 0.7549 (mmt180) REVERT: B 762 MET cc_start: 0.9068 (mmt) cc_final: 0.8640 (mmt) REVERT: B 763 ASP cc_start: 0.8868 (m-30) cc_final: 0.8491 (m-30) REVERT: B 884 GLU cc_start: 0.8792 (pt0) cc_final: 0.8486 (pt0) REVERT: B 887 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8943 (mt) REVERT: B 980 ASP cc_start: 0.8635 (p0) cc_final: 0.8432 (p0) REVERT: B 1111 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 47 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 128 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7896 (p0) REVERT: C 183 PRO cc_start: 0.8788 (Cg_endo) cc_final: 0.8573 (Cg_exo) REVERT: C 248 GLN cc_start: 0.8919 (tt0) cc_final: 0.8432 (tt0) REVERT: C 273 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7904 (p0) REVERT: E 94 LYS cc_start: 0.8279 (tppt) cc_final: 0.7401 (mtmm) REVERT: E 117 THR cc_start: 0.8170 (m) cc_final: 0.7945 (p) REVERT: F 70 LYS cc_start: 0.8825 (tttt) cc_final: 0.8488 (tttm) REVERT: F 114 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: F 124 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8624 (mt-10) REVERT: F 152 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8108 (tp) REVERT: G 72 LYS cc_start: 0.8645 (mptt) cc_final: 0.8214 (mptt) REVERT: I 29 GLU cc_start: 0.7102 (tp30) cc_final: 0.6217 (pt0) REVERT: K 122 LYS cc_start: 0.8754 (tptt) cc_final: 0.8504 (tptp) REVERT: K 138 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7808 (mmmm) outliers start: 105 outliers final: 88 residues processed: 565 average time/residue: 0.2241 time to fit residues: 201.1442 Evaluate side-chains 590 residues out of total 3473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 494 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1224 GLU Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1473 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 25 ARG Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 110 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 326 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 311 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 chunk 336 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 263 ASN A 384 GLN A1323 HIS B 224 ASN B 739 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.142911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.108787 restraints weight = 37704.799| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.36 r_work: 0.2848 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.266 33537 Z= 0.239 Angle : 0.742 59.200 45631 Z= 0.404 Chirality : 0.047 0.506 5097 Planarity : 0.005 0.060 5637 Dihedral : 12.903 87.798 5080 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.05 % Allowed : 15.61 % Favored : 81.34 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 3870 helix: 0.04 (0.15), residues: 1291 sheet: -1.37 (0.21), residues: 570 loop : -0.95 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 634 TYR 0.024 0.002 TYR A1302 PHE 0.025 0.002 PHE B1167 TRP 0.028 0.001 TRP B 836 HIS 0.006 0.001 HIS B 646 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (33513) covalent geometry : angle 0.73661 / 0.40 (45610) hydrogen bonds : bond 0.03790 / 2.48 ( 1092) hydrogen bonds : angle 4.87011 / 3.36 ( 3055) metal coordination : bond 0.00620 / 0.41 ( 24) metal coordination : angle 4.21063 / 2.38 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10790.93 seconds wall clock time: 184 minutes 47.52 seconds (11087.52 seconds total)