Starting phenix.real_space_refine on Sun Aug 9 14:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4b_17404/08_2026/8p4b_17404.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 8 6.06 5 P 81 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 22078 2.51 5 N 6214 2.21 5 O 6787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35383 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11166 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1340} Chain breaks: 5 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9052 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 4 Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 15, 'TRANS': 247} Chain breaks: 1 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 503 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "P" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 475 Classifications: {'RNAv2': 22} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 7} Link IDs: {'rna2p': 5, 'rna3p': 16} Chain: "T" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 711 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 110.345 69.636 79.417 1.00 99.80 S ATOM 486 SG CYS A 74 109.070 65.926 78.574 1.00 95.82 S ATOM 768 SG CYS A 111 96.822 58.639 124.443 1.00132.71 S ATOM 796 SG CYS A 114 98.727 58.269 124.090 1.00130.87 S ATOM 19788 SG CYS B1119 105.794 52.787 87.409 1.00 93.27 S ATOM 19810 SG CYS B1122 104.622 55.620 90.174 1.00 93.70 S ATOM 19925 SG CYS B1137 106.975 56.476 87.690 1.00102.48 S ATOM 19946 SG CYS B1140 107.588 54.089 90.929 1.00106.33 S ATOM 20912 SG CYS C 88 78.136 89.452 21.918 1.00 94.89 S ATOM 20925 SG CYS C 90 80.958 91.136 23.815 1.00101.42 S ATOM 20960 SG CYS C 94 78.997 93.124 21.882 1.00 89.91 S ATOM 20982 SG CYS C 97 77.274 91.868 24.955 1.00 85.03 S ATOM 25965 SG CYS I 17 54.695 106.790 142.566 1.00128.57 S ATOM 25989 SG CYS I 20 58.337 106.788 141.337 1.00127.79 S ATOM 26150 SG CYS I 39 56.990 103.475 142.246 1.00137.49 S ATOM 26175 SG CYS I 42 57.376 106.036 144.977 1.00137.62 S ATOM 26527 SG CYS I 86 23.212 110.857 111.591 1.00117.48 S ATOM 26551 SG CYS I 89 22.667 114.479 110.548 1.00122.40 S ATOM 26755 SG CYS I 114 25.290 112.177 108.752 1.00113.28 S ATOM 26790 SG CYS I 119 25.837 113.500 112.271 1.00119.33 S ATOM 26900 SG CYS J 7 53.896 98.563 45.014 1.00 60.42 S ATOM 27188 SG CYS J 44 49.995 97.454 44.353 1.00 69.31 S ATOM 27194 SG CYS J 45 51.355 100.326 42.356 1.00 67.35 S ATOM 28356 SG CYS L 19 89.980 119.808 58.531 1.00105.74 S ATOM 28375 SG CYS L 22 90.031 122.809 56.200 1.00107.65 S ATOM 28492 SG CYS L 36 93.250 121.263 57.556 1.00116.35 S ATOM 28518 SG CYS L 39 90.757 123.331 59.801 1.00120.48 S Time building chain proxies: 6.28, per 1000 atoms: 0.18 Number of scatterers: 35383 At special positions: 0 Unit cell: (164.85, 145.95, 165.9, 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 8 29.99 S 214 16.00 P 81 15.00 Mg 1 11.99 O 6787 8.00 N 6214 7.00 C 22078 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 30 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7938 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 47 sheets defined 36.4% alpha, 17.9% beta 25 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.605A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.009A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.616A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.860A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.856A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.284A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.533A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 696 through 722 removed outlier: 3.687A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.732A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.539A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.520A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 932 removed outlier: 3.736A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.665A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.690A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.539A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.630A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.102A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.560A pdb=" N VAL A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.849A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1436 through 1446 Processing helix chain 'A' and resid 1454 through 1460 removed outlier: 3.749A pdb=" N MET A1459 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.526A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.465A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.427A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.535A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.712A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.526A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.660A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.943A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.584A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 583 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.828A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.842A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.643A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.835A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.528A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.621A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.645A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.665A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.868A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.589A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.889A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.254A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.965A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.534A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.512A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.840A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.793A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.545A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.716A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.444A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.641A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.759A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.791A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 262 Processing helix chain 'M' and resid 282 through 287 removed outlier: 3.706A pdb=" N LEU M 286 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS M 287 " --> pdb=" O LEU M 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 282 through 287' Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 398 removed outlier: 4.278A pdb=" N SER M 390 " --> pdb=" O ARG M 386 " (cutoff:3.500A) Proline residue: M 391 - end of helix Processing helix chain 'M' and resid 419 through 425 removed outlier: 4.295A pdb=" N LYS M 423 " --> pdb=" O CYS M 419 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 424 " --> pdb=" O THR M 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 508 Processing helix chain 'M' and resid 538 through 551 Processing helix chain 'M' and resid 554 through 564 removed outlier: 3.828A pdb=" N GLU M 560 " --> pdb=" O GLU M 556 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE M 561 " --> pdb=" O MET M 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.690A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.669A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 369 removed outlier: 3.710A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 459 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.771A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.208A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.208A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.610A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 3.617A pdb=" N LEU A1257 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.932A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 127 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.558A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.547A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.587A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR L 17 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC9, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.152A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD2, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.789A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD4, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD5, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.465A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 44 through 55 removed outlier: 5.166A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.421A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.517A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE2, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE3, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.057A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.613A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE G 147 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE9, first strand: chain 'M' and resid 241 through 243 removed outlier: 4.758A pdb=" N VAL M 310 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU M 341 " --> pdb=" O ILE M 365 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLU M 345 " --> pdb=" O ILE M 361 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE M 361 " --> pdb=" O GLU M 345 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE M 347 " --> pdb=" O TYR M 359 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR M 359 " --> pdb=" O ILE M 347 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP M 349 " --> pdb=" O PRO M 357 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL M 351 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N SER M 409 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ARG M 411 " --> pdb=" O PRO M 357 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR M 359 " --> pdb=" O ARG M 411 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 271 through 275 removed outlier: 4.366A pdb=" N VAL M 274 " --> pdb=" O CYS M 453 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP M 455 " --> pdb=" O VAL M 274 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 494 through 501 removed outlier: 7.284A pdb=" N VAL M 491 " --> pdb=" O PRO M 497 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY M 487 " --> pdb=" O ILE M 501 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE M 514 " --> pdb=" O GLN M 529 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN M 529 " --> pdb=" O ILE M 514 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 8.60 Time building geometry restraints manager: 3.28 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: 9080 1.33 - 1.45: 6956 1.45 - 1.58: 19688 1.58 - 1.70: 158 1.70 - 1.82: 339 Bond restraints: 36221 Sorted by residual: bond pdb=" C3' DG N 36 " pdb=" C2' DG N 36 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC T 13 " pdb=" C2' DC T 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C3' DC T 16 " pdb=" C2' DC T 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.24e+00 bond pdb=" C3' DC T 12 " pdb=" C2' DC T 12 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.44e+00 bond pdb=" C3' DT T 14 " pdb=" C2' DT T 14 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.28e+00 ... (remaining 36216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 48705 2.70 - 5.39: 500 5.39 - 8.09: 61 8.09 - 10.78: 10 10.78 - 13.48: 3 Bond angle restraints: 49279 Sorted by residual: angle pdb=" C HIS B 98 " pdb=" N TRP B 99 " pdb=" CA TRP B 99 " ideal model delta sigma weight residual 121.54 132.54 -11.00 1.91e+00 2.74e-01 3.32e+01 angle pdb=" N VAL J 14 " pdb=" CA VAL J 14 " pdb=" C VAL J 14 " ideal model delta sigma weight residual 113.47 108.22 5.25 1.01e+00 9.80e-01 2.70e+01 angle pdb=" CA PRO G 121 " pdb=" N PRO G 121 " pdb=" CD PRO G 121 " ideal model delta sigma weight residual 112.00 104.91 7.09 1.40e+00 5.10e-01 2.57e+01 angle pdb=" N TRP B 99 " pdb=" CA TRP B 99 " pdb=" CB TRP B 99 " ideal model delta sigma weight residual 110.49 118.98 -8.49 1.69e+00 3.50e-01 2.52e+01 angle pdb=" CB MET M 312 " pdb=" CG MET M 312 " pdb=" SD MET M 312 " ideal model delta sigma weight residual 112.70 99.22 13.48 3.00e+00 1.11e-01 2.02e+01 ... (remaining 49274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 21350 34.98 - 69.96: 547 69.96 - 104.94: 40 104.94 - 139.92: 0 139.92 - 174.90: 4 Dihedral angle restraints: 21941 sinusoidal: 9674 harmonic: 12267 Sorted by residual: dihedral pdb=" C4' G P 25 " pdb=" C3' G P 25 " pdb=" C2' G P 25 " pdb=" C1' G P 25 " ideal model delta sinusoidal sigma weight residual 36.34 -39.23 75.57 1 3.10e+00 1.04e-01 7.50e+02 dihedral pdb=" C4' C P 30 " pdb=" C3' C P 30 " pdb=" C2' C P 30 " pdb=" C1' C P 30 " ideal model delta sinusoidal sigma weight residual 36.35 -37.51 73.86 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.87 73.22 1 3.10e+00 1.04e-01 7.11e+02 ... (remaining 21938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4963 0.083 - 0.166: 493 0.166 - 0.248: 45 0.248 - 0.331: 8 0.331 - 0.414: 1 Chirality restraints: 5510 Sorted by residual: chirality pdb=" C3' G P 36 " pdb=" C4' G P 36 " pdb=" O3' G P 36 " pdb=" C2' G P 36 " both_signs ideal model delta sigma weight residual False -2.50 -2.08 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" P A P 39 " pdb=" OP1 A P 39 " pdb=" OP2 A P 39 " pdb=" O5' A P 39 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' G P 36 " pdb=" C3' G P 36 " pdb=" O2' G P 36 " pdb=" C1' G P 36 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5507 not shown) Planarity restraints: 6104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 120 " -0.090 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO G 121 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 81 " 0.043 5.00e-02 4.00e+02 6.37e-02 6.48e+00 pdb=" N PRO H 82 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 82 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 82 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 102 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO G 103 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " -0.029 5.00e-02 4.00e+02 ... (remaining 6101 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 74 2.34 - 2.98: 17181 2.98 - 3.62: 55489 3.62 - 4.26: 85418 4.26 - 4.90: 140460 Nonbonded interactions: 298622 Sorted by model distance: nonbonded pdb=" N6 A P 27 " pdb=" NE2 GLN M 254 " model vdw 1.698 3.200 nonbonded pdb=" OP1 G P 25 " pdb=" N2 G P 25 " model vdw 1.990 3.120 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.088 2.170 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2003 " model vdw 2.129 2.170 nonbonded pdb=" O LYS A 42 " pdb=" ND2 ASN A 288 " model vdw 2.144 3.120 ... (remaining 298617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 35.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.004 0.334 36249 Z= 0.207 Angle : 0.743 22.613 49309 Z= 0.412 Chirality : 0.050 0.414 5510 Planarity : 0.005 0.132 6104 Dihedral : 14.729 174.897 14003 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.88 (0.13), residues: 4169 helix: 0.30 (0.14), residues: 1380 sheet: -0.81 (0.21), residues: 583 loop : -1.06 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 70 TYR 0.033 0.002 TYR B 752 PHE 0.025 0.002 PHE G 44 TRP 0.024 0.002 TRP B 99 HIS 0.006 0.001 HIS B 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.20 (36221) covalent geometry : angle 0.72126 / 0.41 (49279) hydrogen bonds : bond 0.18823 / 12.15 ( 1383) hydrogen bonds : angle 7.06929 / 5.14 ( 3834) metal coordination : bond 0.06419 / 3.81 ( 28) metal coordination : angle 7.22592 / 3.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 559 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 MET cc_start: 0.8485 (mtm) cc_final: 0.8240 (mtt) REVERT: A 1303 GLN cc_start: 0.8636 (tt0) cc_final: 0.8228 (tm-30) REVERT: A 1344 MET cc_start: 0.7779 (tpt) cc_final: 0.7534 (tpp) REVERT: E 94 MET cc_start: 0.7866 (mmm) cc_final: 0.7485 (mmm) REVERT: E 125 TYR cc_start: 0.7274 (m-80) cc_final: 0.6857 (m-10) REVERT: F 80 MET cc_start: 0.8632 (mmp) cc_final: 0.8406 (mmm) REVERT: H 90 TYR cc_start: 0.8745 (t80) cc_final: 0.8403 (t80) REVERT: H 118 TYR cc_start: 0.9230 (m-80) cc_final: 0.8426 (m-80) REVERT: I 23 MET cc_start: 0.7807 (ttp) cc_final: 0.7578 (ttp) REVERT: I 34 ILE cc_start: 0.8884 (tp) cc_final: 0.8654 (tp) REVERT: I 44 TYR cc_start: 0.8049 (t80) cc_final: 0.7789 (t80) REVERT: I 57 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8570 (mmmt) REVERT: I 71 ASP cc_start: 0.8514 (p0) cc_final: 0.8199 (p0) REVERT: D 31 THR cc_start: 0.8913 (m) cc_final: 0.7971 (t) REVERT: D 95 PHE cc_start: 0.8822 (t80) cc_final: 0.8434 (t80) REVERT: G 3 TYR cc_start: 0.7574 (m-80) cc_final: 0.5948 (m-80) REVERT: G 27 LYS cc_start: 0.8402 (mttt) cc_final: 0.8028 (mptt) REVERT: G 80 PHE cc_start: 0.6283 (m-10) cc_final: 0.5218 (m-10) REVERT: G 86 ASP cc_start: 0.7373 (m-30) cc_final: 0.6751 (t0) REVERT: G 158 PHE cc_start: 0.8347 (m-80) cc_final: 0.7908 (m-80) REVERT: M 299 ARG cc_start: 0.7229 (mmt180) cc_final: 0.6661 (mmm160) REVERT: M 309 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7396 (mt-10) REVERT: M 346 MET cc_start: -0.0913 (mmt) cc_final: -0.1174 (mmt) REVERT: M 442 PHE cc_start: 0.9338 (m-10) cc_final: 0.9090 (m-10) REVERT: M 490 TYR cc_start: 0.7750 (m-80) cc_final: 0.7501 (m-10) REVERT: M 557 MET cc_start: 0.2619 (ttt) cc_final: 0.2343 (ttt) REVERT: M 564 ARG cc_start: 0.2964 (ptt180) cc_final: 0.2395 (mtm180) outliers start: 1 outliers final: 0 residues processed: 560 average time/residue: 0.2153 time to fit residues: 193.4166 Evaluate side-chains 398 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 905 ASN A1299 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 725 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1071 ASN B1117 HIS H 46 GLN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN L 23 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 547 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.096667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064372 restraints weight = 85699.210| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.21 r_work: 0.2867 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36249 Z= 0.167 Angle : 0.759 19.585 49309 Z= 0.377 Chirality : 0.056 1.025 5510 Planarity : 0.005 0.083 6104 Dihedral : 13.534 171.083 5473 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 0.73 % Allowed : 7.77 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4169 helix: 0.44 (0.14), residues: 1398 sheet: -0.77 (0.21), residues: 575 loop : -1.00 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 67 TYR 0.025 0.002 TYR M 494 PHE 0.020 0.002 PHE A 113 TRP 0.046 0.002 TRP B 99 HIS 0.015 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (36221) covalent geometry : angle 0.74963 / 0.38 (49279) hydrogen bonds : bond 0.05321 / 3.60 ( 1383) hydrogen bonds : angle 5.68455 / 4.12 ( 3834) metal coordination : bond 0.00735 / 0.48 ( 28) metal coordination : angle 4.79521 / 2.96 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 432 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8221 (t0) cc_final: 0.7965 (t0) REVERT: A 986 MET cc_start: 0.9425 (mtm) cc_final: 0.8983 (mtt) REVERT: A 1086 MET cc_start: 0.9189 (mmm) cc_final: 0.8929 (mmm) REVERT: A 1166 LEU cc_start: 0.9218 (tt) cc_final: 0.8994 (tt) REVERT: A 1303 GLN cc_start: 0.9166 (tt0) cc_final: 0.8310 (tm-30) REVERT: B 954 MET cc_start: 0.9212 (tpp) cc_final: 0.8986 (mmt) REVERT: E 94 MET cc_start: 0.8538 (mmm) cc_final: 0.8034 (mmm) REVERT: E 125 TYR cc_start: 0.7519 (m-80) cc_final: 0.7308 (m-10) REVERT: F 80 MET cc_start: 0.8991 (mmp) cc_final: 0.8676 (mmm) REVERT: F 86 GLU cc_start: 0.7640 (pm20) cc_final: 0.7321 (pm20) REVERT: H 90 TYR cc_start: 0.9242 (t80) cc_final: 0.8638 (t80) REVERT: H 118 TYR cc_start: 0.9436 (m-80) cc_final: 0.9223 (m-80) REVERT: I 40 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7588 (mtt90) REVERT: I 74 GLN cc_start: 0.8862 (pm20) cc_final: 0.8653 (pm20) REVERT: I 83 ASP cc_start: 0.8913 (p0) cc_final: 0.8322 (p0) REVERT: I 84 HIS cc_start: 0.9049 (m170) cc_final: 0.8627 (m170) REVERT: K 16 GLU cc_start: 0.7591 (tt0) cc_final: 0.7308 (tt0) REVERT: D 39 MET cc_start: 0.9167 (ptm) cc_final: 0.8868 (ptt) REVERT: D 70 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.7996 (ttp-170) REVERT: G 1 MET cc_start: 0.7647 (ttt) cc_final: 0.7087 (ttt) REVERT: G 3 TYR cc_start: 0.8140 (m-80) cc_final: 0.6332 (m-80) REVERT: G 24 ASN cc_start: 0.8892 (t0) cc_final: 0.8568 (t0) REVERT: G 28 GLN cc_start: 0.8915 (mt0) cc_final: 0.8662 (mm-40) REVERT: G 80 PHE cc_start: 0.6624 (m-10) cc_final: 0.5725 (m-10) REVERT: G 85 VAL cc_start: 0.9019 (p) cc_final: 0.8776 (p) REVERT: G 144 ARG cc_start: 0.7424 (mpp80) cc_final: 0.6817 (mtt90) REVERT: G 151 ARG cc_start: 0.7410 (ptm-80) cc_final: 0.7109 (ptm-80) REVERT: G 158 PHE cc_start: 0.8823 (m-80) cc_final: 0.8453 (m-80) REVERT: M 299 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6910 (mmm160) REVERT: M 309 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7286 (mt-10) REVERT: M 490 TYR cc_start: 0.7843 (m-80) cc_final: 0.7633 (m-80) REVERT: M 494 TYR cc_start: 0.8213 (t80) cc_final: 0.7958 (t80) REVERT: M 564 ARG cc_start: 0.3311 (ptt180) cc_final: 0.2798 (mtm180) outliers start: 27 outliers final: 17 residues processed: 448 average time/residue: 0.2064 time to fit residues: 148.7969 Evaluate side-chains 404 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 386 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain M residue 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 373 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 405 optimal weight: 30.0000 chunk 201 optimal weight: 3.9990 chunk 377 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 167 optimal weight: 0.0370 chunk 135 optimal weight: 2.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 593 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN C 123 ASN I 32 ASN I 100 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.095563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062696 restraints weight = 85278.850| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.18 r_work: 0.2831 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 36249 Z= 0.223 Angle : 0.712 12.802 49309 Z= 0.360 Chirality : 0.051 0.810 5510 Planarity : 0.005 0.060 6104 Dihedral : 13.594 171.925 5473 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 1.77 % Allowed : 9.67 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.59 (0.13), residues: 4169 helix: 0.68 (0.14), residues: 1381 sheet: -0.70 (0.20), residues: 596 loop : -0.97 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 33 TYR 0.029 0.002 TYR I 54 PHE 0.023 0.002 PHE G 107 TRP 0.074 0.002 TRP B 99 HIS 0.011 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (36221) covalent geometry : angle 0.70408 / 0.36 (49279) hydrogen bonds : bond 0.04701 / 3.17 ( 1383) hydrogen bonds : angle 5.34491 / 3.86 ( 3834) metal coordination : bond 0.00752 / 0.48 ( 28) metal coordination : angle 4.45398 / 2.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 426 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8244 (t0) cc_final: 0.8016 (t0) REVERT: A 327 ARG cc_start: 0.8845 (mpt90) cc_final: 0.8639 (mpt90) REVERT: A 930 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8836 (tt) REVERT: A 1166 LEU cc_start: 0.9239 (tt) cc_final: 0.8934 (tt) REVERT: A 1411 LEU cc_start: 0.9373 (mt) cc_final: 0.9147 (mt) REVERT: A 1441 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 954 MET cc_start: 0.9348 (tpp) cc_final: 0.9103 (mmt) REVERT: E 18 MET cc_start: 0.9291 (mmm) cc_final: 0.9086 (mmm) REVERT: F 80 MET cc_start: 0.8995 (mmp) cc_final: 0.8627 (mmp) REVERT: H 48 TYR cc_start: 0.9260 (t80) cc_final: 0.8860 (t80) REVERT: H 90 TYR cc_start: 0.9319 (t80) cc_final: 0.8791 (t80) REVERT: I 74 GLN cc_start: 0.8879 (pm20) cc_final: 0.8595 (pm20) REVERT: I 83 ASP cc_start: 0.8910 (p0) cc_final: 0.8337 (p0) REVERT: I 84 HIS cc_start: 0.9073 (m170) cc_final: 0.8582 (m170) REVERT: I 108 MET cc_start: 0.8885 (mmm) cc_final: 0.8640 (mmm) REVERT: K 39 ASP cc_start: 0.9090 (p0) cc_final: 0.8850 (p0) REVERT: D 39 MET cc_start: 0.9122 (ptm) cc_final: 0.8829 (ptt) REVERT: D 70 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8000 (ttp-170) REVERT: D 93 HIS cc_start: 0.8843 (t-170) cc_final: 0.8635 (t70) REVERT: G 1 MET cc_start: 0.7689 (ttt) cc_final: 0.7383 (ttm) REVERT: G 24 ASN cc_start: 0.8856 (t0) cc_final: 0.8213 (t0) REVERT: G 28 GLN cc_start: 0.8938 (mt0) cc_final: 0.8392 (mt0) REVERT: G 80 PHE cc_start: 0.6769 (m-10) cc_final: 0.6211 (m-10) REVERT: G 86 ASP cc_start: 0.7154 (m-30) cc_final: 0.6673 (m-30) REVERT: G 158 PHE cc_start: 0.8823 (m-80) cc_final: 0.8394 (m-80) REVERT: M 276 MET cc_start: 0.7641 (mmm) cc_final: 0.6897 (mmm) REVERT: M 309 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7364 (mt-10) REVERT: M 346 MET cc_start: -0.1582 (mmt) cc_final: -0.1816 (mmt) REVERT: M 490 TYR cc_start: 0.7870 (m-80) cc_final: 0.7658 (m-80) REVERT: M 494 TYR cc_start: 0.8299 (t80) cc_final: 0.7867 (t80) REVERT: M 543 MET cc_start: 0.9131 (mmt) cc_final: 0.8900 (mmt) outliers start: 66 outliers final: 37 residues processed: 468 average time/residue: 0.2281 time to fit residues: 174.1367 Evaluate side-chains 424 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 386 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 453 CYS Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 517 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 143 optimal weight: 7.9990 chunk 293 optimal weight: 7.9990 chunk 413 optimal weight: 20.0000 chunk 407 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 356 optimal weight: 40.0000 chunk 70 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 404 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 525 ASN B1071 ASN C 66 HIS ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.093809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060993 restraints weight = 84671.698| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.13 r_work: 0.2788 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 36249 Z= 0.273 Angle : 0.716 10.597 49309 Z= 0.361 Chirality : 0.050 0.499 5510 Planarity : 0.004 0.066 6104 Dihedral : 13.571 172.180 5473 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.91 % Allowed : 11.31 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.50 (0.13), residues: 4169 helix: 0.81 (0.14), residues: 1369 sheet: -0.72 (0.21), residues: 593 loop : -0.93 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 33 TYR 0.023 0.002 TYR B 388 PHE 0.025 0.002 PHE A 458 TRP 0.042 0.002 TRP B 99 HIS 0.006 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.27 (36221) covalent geometry : angle 0.70787 / 0.36 (49279) hydrogen bonds : bond 0.04475 / 3.00 ( 1383) hydrogen bonds : angle 5.24271 / 3.78 ( 3834) metal coordination : bond 0.00907 / 0.58 ( 28) metal coordination : angle 4.54131 / 3.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 392 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8318 (t0) cc_final: 0.8111 (t0) REVERT: A 565 MET cc_start: 0.9415 (mmm) cc_final: 0.9211 (mmm) REVERT: A 1166 LEU cc_start: 0.9290 (tt) cc_final: 0.9012 (tt) REVERT: A 1411 LEU cc_start: 0.9404 (mt) cc_final: 0.9153 (mt) REVERT: A 1441 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 668 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8736 (mm) REVERT: B 954 MET cc_start: 0.9391 (tpp) cc_final: 0.9157 (mmt) REVERT: C 27 ASP cc_start: 0.8723 (m-30) cc_final: 0.8406 (m-30) REVERT: E 94 MET cc_start: 0.8344 (mmm) cc_final: 0.8053 (mmm) REVERT: F 80 MET cc_start: 0.9024 (mmp) cc_final: 0.8812 (mmm) REVERT: H 48 TYR cc_start: 0.9294 (t80) cc_final: 0.8910 (t80) REVERT: H 90 TYR cc_start: 0.9346 (t80) cc_final: 0.8837 (t80) REVERT: I 47 GLU cc_start: 0.7940 (pp20) cc_final: 0.7529 (pp20) REVERT: I 60 HIS cc_start: 0.8146 (t70) cc_final: 0.7860 (t70) REVERT: I 74 GLN cc_start: 0.8915 (pm20) cc_final: 0.8601 (pm20) REVERT: K 39 ASP cc_start: 0.9073 (p0) cc_final: 0.8843 (p0) REVERT: D 39 MET cc_start: 0.9241 (ptm) cc_final: 0.8916 (ptt) REVERT: D 70 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7763 (ttp-170) REVERT: G 1 MET cc_start: 0.7883 (ttt) cc_final: 0.7326 (ttm) REVERT: G 2 PHE cc_start: 0.8029 (m-10) cc_final: 0.7555 (m-10) REVERT: G 3 TYR cc_start: 0.7671 (m-80) cc_final: 0.6657 (m-80) REVERT: G 9 HIS cc_start: 0.8807 (t70) cc_final: 0.8592 (t70) REVERT: G 24 ASN cc_start: 0.8856 (t0) cc_final: 0.8617 (t0) REVERT: G 27 LYS cc_start: 0.8510 (mttt) cc_final: 0.8269 (mmtt) REVERT: G 33 GLU cc_start: 0.8782 (tt0) cc_final: 0.8538 (tt0) REVERT: G 80 PHE cc_start: 0.7016 (m-10) cc_final: 0.6101 (m-10) REVERT: G 91 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7125 (tm-30) REVERT: G 94 LYS cc_start: 0.6894 (mmtt) cc_final: 0.5835 (pttt) REVERT: G 97 LEU cc_start: 0.9180 (tp) cc_final: 0.8952 (tp) REVERT: G 98 PHE cc_start: 0.8837 (m-10) cc_final: 0.8422 (m-10) REVERT: G 110 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7836 (ttt180) REVERT: G 158 PHE cc_start: 0.8882 (m-80) cc_final: 0.8477 (m-80) REVERT: M 276 MET cc_start: 0.7823 (mmm) cc_final: 0.6937 (mmm) REVERT: M 309 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7279 (mt-10) REVERT: M 490 TYR cc_start: 0.7882 (m-80) cc_final: 0.7545 (m-10) REVERT: M 494 TYR cc_start: 0.8170 (t80) cc_final: 0.7874 (t80) REVERT: M 543 MET cc_start: 0.9164 (mmt) cc_final: 0.8919 (mmt) outliers start: 71 outliers final: 41 residues processed: 444 average time/residue: 0.2122 time to fit residues: 154.4390 Evaluate side-chains 421 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 407 optimal weight: 30.0000 chunk 180 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 525 ASN B1071 ASN I 32 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062939 restraints weight = 84325.864| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.15 r_work: 0.2831 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36249 Z= 0.153 Angle : 0.656 10.160 49309 Z= 0.330 Chirality : 0.047 0.416 5510 Planarity : 0.004 0.057 6104 Dihedral : 13.552 171.004 5473 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 1.99 % Allowed : 12.07 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.41 (0.13), residues: 4169 helix: 0.91 (0.15), residues: 1372 sheet: -0.72 (0.21), residues: 575 loop : -0.88 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 24 TYR 0.022 0.002 TYR I 44 PHE 0.026 0.002 PHE G 107 TRP 0.024 0.002 TRP B 99 HIS 0.008 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (36221) covalent geometry : angle 0.64903 / 0.33 (49279) hydrogen bonds : bond 0.04170 / 2.79 ( 1383) hydrogen bonds : angle 5.09538 / 3.67 ( 3834) metal coordination : bond 0.00666 / 0.44 ( 28) metal coordination : angle 4.03421 / 2.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 411 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8898 (tt) REVERT: A 1086 MET cc_start: 0.9143 (mmm) cc_final: 0.8912 (mmm) REVERT: A 1166 LEU cc_start: 0.9230 (tt) cc_final: 0.8924 (tt) REVERT: A 1396 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.8140 (mmt-90) REVERT: A 1411 LEU cc_start: 0.9355 (mt) cc_final: 0.9150 (mt) REVERT: B 668 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (mm) REVERT: B 692 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8817 (p) REVERT: B 954 MET cc_start: 0.9335 (tpp) cc_final: 0.9124 (mmt) REVERT: C 27 ASP cc_start: 0.8679 (m-30) cc_final: 0.8340 (m-30) REVERT: E 94 MET cc_start: 0.8411 (mmm) cc_final: 0.8177 (mmm) REVERT: F 80 MET cc_start: 0.9067 (mmp) cc_final: 0.8815 (mmm) REVERT: H 48 TYR cc_start: 0.9237 (t80) cc_final: 0.8889 (t80) REVERT: H 90 TYR cc_start: 0.9330 (t80) cc_final: 0.8791 (t80) REVERT: I 60 HIS cc_start: 0.8197 (t70) cc_final: 0.7824 (t70) REVERT: I 74 GLN cc_start: 0.8932 (pm20) cc_final: 0.8617 (pm20) REVERT: K 97 GLU cc_start: 0.8755 (tt0) cc_final: 0.8402 (tt0) REVERT: D 31 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.7624 (t) REVERT: D 39 MET cc_start: 0.9275 (ptm) cc_final: 0.8952 (ptt) REVERT: D 70 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7989 (ttp-170) REVERT: D 93 HIS cc_start: 0.9159 (t-90) cc_final: 0.8952 (t-90) REVERT: D 95 PHE cc_start: 0.8853 (t80) cc_final: 0.8442 (t80) REVERT: G 2 PHE cc_start: 0.7859 (m-10) cc_final: 0.7604 (m-10) REVERT: G 3 TYR cc_start: 0.7536 (m-80) cc_final: 0.6268 (m-80) REVERT: G 24 ASN cc_start: 0.8752 (t0) cc_final: 0.8544 (t0) REVERT: G 80 PHE cc_start: 0.7077 (m-10) cc_final: 0.6170 (m-10) REVERT: G 86 ASP cc_start: 0.6689 (m-30) cc_final: 0.5748 (m-30) REVERT: G 94 LYS cc_start: 0.6788 (mmtt) cc_final: 0.5695 (pttt) REVERT: G 97 LEU cc_start: 0.9171 (tp) cc_final: 0.8818 (tp) REVERT: G 158 PHE cc_start: 0.8872 (m-80) cc_final: 0.8424 (m-80) REVERT: M 276 MET cc_start: 0.7926 (mmm) cc_final: 0.6907 (mmm) REVERT: M 309 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7296 (mt-10) REVERT: M 490 TYR cc_start: 0.7753 (m-80) cc_final: 0.7446 (m-10) REVERT: M 494 TYR cc_start: 0.8132 (t80) cc_final: 0.7805 (t80) REVERT: M 539 TYR cc_start: 0.9257 (p90) cc_final: 0.8969 (p90) REVERT: M 543 MET cc_start: 0.9161 (mmt) cc_final: 0.8908 (mmt) outliers start: 74 outliers final: 44 residues processed: 467 average time/residue: 0.2106 time to fit residues: 159.7145 Evaluate side-chains 430 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 238 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 355 optimal weight: 40.0000 chunk 301 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 382 optimal weight: 20.0000 chunk 379 optimal weight: 2.9990 chunk 194 optimal weight: 0.0170 chunk 105 optimal weight: 10.0000 chunk 411 optimal weight: 0.8980 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 525 ASN B1071 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062132 restraints weight = 84593.064| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.17 r_work: 0.2819 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36249 Z= 0.182 Angle : 0.662 10.683 49309 Z= 0.332 Chirality : 0.047 0.356 5510 Planarity : 0.004 0.081 6104 Dihedral : 13.551 170.773 5473 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 2.36 % Allowed : 13.17 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.35 (0.13), residues: 4169 helix: 0.97 (0.15), residues: 1376 sheet: -0.78 (0.21), residues: 566 loop : -0.83 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1141 TYR 0.021 0.002 TYR B 388 PHE 0.030 0.002 PHE G 107 TRP 0.028 0.002 TRP A1210 HIS 0.005 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (36221) covalent geometry : angle 0.65438 / 0.33 (49279) hydrogen bonds : bond 0.04084 / 2.70 ( 1383) hydrogen bonds : angle 5.02247 / 3.61 ( 3834) metal coordination : bond 0.00678 / 0.42 ( 28) metal coordination : angle 4.13202 / 2.89 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 403 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8773 (m) REVERT: A 322 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8149 (mt) REVERT: A 905 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8511 (t0) REVERT: A 930 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8907 (tt) REVERT: A 986 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9191 (mtp) REVERT: A 1086 MET cc_start: 0.9133 (mmm) cc_final: 0.8922 (mmm) REVERT: A 1153 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8098 (mtm-85) REVERT: A 1166 LEU cc_start: 0.9237 (tt) cc_final: 0.8934 (tt) REVERT: A 1221 MET cc_start: 0.8903 (tpp) cc_final: 0.8566 (tpp) REVERT: B 668 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (mm) REVERT: B 692 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8836 (p) REVERT: B 954 MET cc_start: 0.9352 (tpp) cc_final: 0.9118 (mmt) REVERT: C 27 ASP cc_start: 0.8704 (m-30) cc_final: 0.8355 (m-30) REVERT: E 94 MET cc_start: 0.8370 (mmm) cc_final: 0.8079 (mmm) REVERT: F 80 MET cc_start: 0.9094 (mmp) cc_final: 0.8872 (mmm) REVERT: H 48 TYR cc_start: 0.9258 (t80) cc_final: 0.8859 (t80) REVERT: H 90 TYR cc_start: 0.9325 (t80) cc_final: 0.8798 (t80) REVERT: H 98 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8522 (ttm-80) REVERT: I 27 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7851 (mmtm) REVERT: I 74 GLN cc_start: 0.8928 (pm20) cc_final: 0.8598 (pm20) REVERT: K 97 GLU cc_start: 0.8778 (tt0) cc_final: 0.8408 (tt0) REVERT: L 47 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8129 (mmmm) REVERT: D 31 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.7947 (t) REVERT: D 39 MET cc_start: 0.9275 (ptm) cc_final: 0.8957 (ptt) REVERT: D 70 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.7992 (ttp-170) REVERT: D 93 HIS cc_start: 0.9161 (t-90) cc_final: 0.8910 (t-170) REVERT: D 95 PHE cc_start: 0.8861 (t80) cc_final: 0.8602 (t80) REVERT: G 2 PHE cc_start: 0.8029 (m-10) cc_final: 0.7215 (m-10) REVERT: G 3 TYR cc_start: 0.7943 (m-80) cc_final: 0.6359 (m-80) REVERT: G 24 ASN cc_start: 0.8753 (t0) cc_final: 0.8545 (t0) REVERT: G 80 PHE cc_start: 0.7099 (m-10) cc_final: 0.6073 (m-10) REVERT: G 86 ASP cc_start: 0.6811 (m-30) cc_final: 0.5838 (m-30) REVERT: G 94 LYS cc_start: 0.6943 (mmtt) cc_final: 0.5951 (pttt) REVERT: G 158 PHE cc_start: 0.8903 (m-80) cc_final: 0.8453 (m-80) REVERT: G 170 LEU cc_start: 0.8825 (tp) cc_final: 0.8618 (tp) REVERT: M 247 GLN cc_start: 0.7514 (mp10) cc_final: 0.6170 (pt0) REVERT: M 276 MET cc_start: 0.8030 (mmm) cc_final: 0.7061 (mmm) REVERT: M 309 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7333 (mt-10) REVERT: M 490 TYR cc_start: 0.7761 (m-80) cc_final: 0.7534 (m-80) REVERT: M 494 TYR cc_start: 0.8093 (t80) cc_final: 0.7739 (t80) REVERT: M 543 MET cc_start: 0.9164 (mmt) cc_final: 0.8916 (mmt) REVERT: M 564 ARG cc_start: 0.3238 (ptt180) cc_final: 0.2709 (mtm180) outliers start: 88 outliers final: 58 residues processed: 468 average time/residue: 0.2324 time to fit residues: 177.1973 Evaluate side-chains 444 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 378 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 488 LEU Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 282 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 422 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 394 optimal weight: 20.0000 chunk 331 optimal weight: 0.5980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 790 GLN A1313 GLN B 144 HIS B 525 ASN B1071 ASN ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061579 restraints weight = 84806.452| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.15 r_work: 0.2799 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36249 Z= 0.217 Angle : 0.682 16.039 49309 Z= 0.341 Chirality : 0.047 0.329 5510 Planarity : 0.004 0.063 6104 Dihedral : 13.567 171.093 5473 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 2.36 % Allowed : 14.06 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.13), residues: 4169 helix: 0.96 (0.14), residues: 1382 sheet: -0.72 (0.21), residues: 580 loop : -0.85 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1141 TYR 0.021 0.002 TYR B 388 PHE 0.023 0.002 PHE M 367 TRP 0.028 0.002 TRP A1210 HIS 0.029 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (36221) covalent geometry : angle 0.67423 / 0.34 (49279) hydrogen bonds : bond 0.04084 / 2.70 ( 1383) hydrogen bonds : angle 5.04381 / 3.63 ( 3834) metal coordination : bond 0.00866 / 0.57 ( 28) metal coordination : angle 4.12393 / 2.90 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 390 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8811 (m) REVERT: A 322 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8168 (mt) REVERT: A 905 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8527 (t0) REVERT: A 930 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9030 (tt) REVERT: A 1166 LEU cc_start: 0.9265 (tt) cc_final: 0.8959 (tt) REVERT: A 1396 ARG cc_start: 0.8371 (mmt-90) cc_final: 0.8161 (mmt-90) REVERT: B 36 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 668 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8602 (mm) REVERT: B 692 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 954 MET cc_start: 0.9375 (tpp) cc_final: 0.9117 (mmt) REVERT: C 41 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: E 94 MET cc_start: 0.8437 (mmm) cc_final: 0.8114 (mmm) REVERT: F 80 MET cc_start: 0.9076 (mmp) cc_final: 0.8874 (mmm) REVERT: F 100 ARG cc_start: 0.9015 (mtp85) cc_final: 0.8652 (mtp180) REVERT: H 31 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: H 48 TYR cc_start: 0.9307 (t80) cc_final: 0.8923 (t80) REVERT: H 90 TYR cc_start: 0.9347 (t80) cc_final: 0.8865 (t80) REVERT: I 40 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6933 (ptp-170) REVERT: I 47 GLU cc_start: 0.7547 (pp20) cc_final: 0.7064 (pp20) REVERT: I 74 GLN cc_start: 0.8933 (pm20) cc_final: 0.8591 (pm20) REVERT: I 108 MET cc_start: 0.8774 (mmm) cc_final: 0.8413 (mmm) REVERT: D 39 MET cc_start: 0.9259 (ptm) cc_final: 0.8950 (ptt) REVERT: D 70 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.7918 (ttp-170) REVERT: G 24 ASN cc_start: 0.8773 (t0) cc_final: 0.8560 (t0) REVERT: G 80 PHE cc_start: 0.7223 (m-10) cc_final: 0.6992 (m-10) REVERT: G 158 PHE cc_start: 0.8898 (m-80) cc_final: 0.8414 (m-80) REVERT: M 247 GLN cc_start: 0.7383 (mp10) cc_final: 0.6095 (pt0) REVERT: M 276 MET cc_start: 0.8041 (mmm) cc_final: 0.6786 (mmm) REVERT: M 309 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7224 (mt-10) REVERT: M 335 MET cc_start: 0.6731 (tpp) cc_final: 0.6027 (ptm) REVERT: M 490 TYR cc_start: 0.7728 (m-80) cc_final: 0.7500 (m-80) REVERT: M 494 TYR cc_start: 0.8156 (t80) cc_final: 0.7775 (t80) REVERT: M 564 ARG cc_start: 0.3245 (ptt180) cc_final: 0.2686 (mtm180) outliers start: 88 outliers final: 55 residues processed: 457 average time/residue: 0.2329 time to fit residues: 174.4094 Evaluate side-chains 444 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 488 LEU Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 180 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 410 optimal weight: 8.9990 chunk 413 optimal weight: 9.9990 chunk 351 optimal weight: 0.8980 chunk 381 optimal weight: 1.9990 chunk 358 optimal weight: 50.0000 chunk 361 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 525 ASN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.094977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062063 restraints weight = 84485.729| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.17 r_work: 0.2817 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36249 Z= 0.165 Angle : 0.667 12.102 49309 Z= 0.335 Chirality : 0.047 0.306 5510 Planarity : 0.004 0.055 6104 Dihedral : 13.572 170.247 5473 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 2.12 % Allowed : 14.65 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.34 (0.13), residues: 4169 helix: 1.00 (0.14), residues: 1380 sheet: -0.75 (0.21), residues: 599 loop : -0.84 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 33 TYR 0.021 0.002 TYR E 125 PHE 0.022 0.001 PHE B 309 TRP 0.031 0.002 TRP A1210 HIS 0.005 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (36221) covalent geometry : angle 0.65962 / 0.33 (49279) hydrogen bonds : bond 0.03983 / 2.64 ( 1383) hydrogen bonds : angle 4.99317 / 3.59 ( 3834) metal coordination : bond 0.00679 / 0.43 ( 28) metal coordination : angle 3.94512 / 2.79 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 394 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8799 (m) REVERT: A 322 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8186 (mt) REVERT: A 905 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8512 (t0) REVERT: A 930 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9028 (tt) REVERT: A 1166 LEU cc_start: 0.9249 (tt) cc_final: 0.8948 (tt) REVERT: A 1396 ARG cc_start: 0.8354 (mmt-90) cc_final: 0.8121 (mmt-90) REVERT: A 1439 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9050 (mm) REVERT: B 36 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 668 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 692 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8826 (p) REVERT: B 954 MET cc_start: 0.9352 (tpp) cc_final: 0.9073 (mmt) REVERT: E 94 MET cc_start: 0.8426 (mmm) cc_final: 0.8102 (mmm) REVERT: F 100 ARG cc_start: 0.8991 (mtp85) cc_final: 0.8624 (mtp180) REVERT: H 20 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.8965 (ttmm) REVERT: H 31 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: H 48 TYR cc_start: 0.9272 (t80) cc_final: 0.8884 (t80) REVERT: H 90 TYR cc_start: 0.9310 (t80) cc_final: 0.8773 (t80) REVERT: I 11 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6419 (t80) REVERT: I 40 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7097 (ptp-170) REVERT: I 74 GLN cc_start: 0.8936 (pm20) cc_final: 0.8584 (pm20) REVERT: I 108 MET cc_start: 0.8734 (mmm) cc_final: 0.8374 (mmm) REVERT: L 16 ILE cc_start: 0.9145 (tp) cc_final: 0.8927 (tp) REVERT: L 47 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8080 (mmmm) REVERT: D 33 LEU cc_start: 0.8829 (mm) cc_final: 0.8467 (tp) REVERT: D 39 MET cc_start: 0.9268 (ptm) cc_final: 0.8944 (ptt) REVERT: D 70 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.7849 (ttp-170) REVERT: G 1 MET cc_start: 0.7858 (tmm) cc_final: 0.7418 (ppp) REVERT: G 3 TYR cc_start: 0.7805 (m-80) cc_final: 0.7346 (m-80) REVERT: G 24 ASN cc_start: 0.8749 (t0) cc_final: 0.8532 (t0) REVERT: G 80 PHE cc_start: 0.7524 (m-10) cc_final: 0.6448 (m-10) REVERT: G 94 LYS cc_start: 0.6525 (mmpt) cc_final: 0.5528 (pttt) REVERT: G 121 PRO cc_start: 0.6884 (Cg_exo) cc_final: 0.6622 (Cg_exo) REVERT: G 158 PHE cc_start: 0.8996 (m-80) cc_final: 0.8534 (m-80) REVERT: M 247 GLN cc_start: 0.7434 (mp10) cc_final: 0.6217 (pt0) REVERT: M 276 MET cc_start: 0.8041 (mmm) cc_final: 0.7037 (mmm) REVERT: M 309 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7202 (mt-10) REVERT: M 335 MET cc_start: 0.6685 (tpp) cc_final: 0.6078 (ptm) REVERT: M 494 TYR cc_start: 0.8087 (t80) cc_final: 0.7649 (t80) outliers start: 79 outliers final: 57 residues processed: 451 average time/residue: 0.2331 time to fit residues: 172.0702 Evaluate side-chains 454 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 386 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 488 LEU Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 340 optimal weight: 0.2980 chunk 377 optimal weight: 9.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN B 525 ASN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN L 26 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.094762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061878 restraints weight = 84322.082| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.15 r_work: 0.2815 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36249 Z= 0.177 Angle : 0.673 12.137 49309 Z= 0.337 Chirality : 0.047 0.290 5510 Planarity : 0.004 0.053 6104 Dihedral : 13.581 169.516 5473 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 2.20 % Allowed : 14.86 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.13), residues: 4169 helix: 0.96 (0.14), residues: 1389 sheet: -0.80 (0.21), residues: 596 loop : -0.83 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 109 TYR 0.024 0.002 TYR E 125 PHE 0.023 0.001 PHE B 309 TRP 0.032 0.002 TRP A1210 HIS 0.015 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (36221) covalent geometry : angle 0.66551 / 0.34 (49279) hydrogen bonds : bond 0.03969 / 2.62 ( 1383) hydrogen bonds : angle 4.99261 / 3.60 ( 3834) metal coordination : bond 0.00692 / 0.44 ( 28) metal coordination : angle 4.03834 / 2.93 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 398 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8789 (m) REVERT: A 322 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8199 (mt) REVERT: A 905 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8518 (t0) REVERT: A 930 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9030 (tt) REVERT: A 1166 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8989 (tt) REVERT: A 1221 MET cc_start: 0.8974 (tpp) cc_final: 0.8395 (tpp) REVERT: A 1396 ARG cc_start: 0.8358 (mmt-90) cc_final: 0.8089 (mmt-90) REVERT: A 1439 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9051 (mm) REVERT: B 36 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 668 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 692 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8846 (p) REVERT: B 954 MET cc_start: 0.9356 (tpp) cc_final: 0.9068 (mmt) REVERT: C 94 CYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7112 (p) REVERT: C 111 GLN cc_start: 0.8219 (mp10) cc_final: 0.7995 (mp10) REVERT: E 90 TYR cc_start: 0.9517 (m-80) cc_final: 0.9228 (m-80) REVERT: E 94 MET cc_start: 0.8445 (mmm) cc_final: 0.8140 (mmm) REVERT: F 100 ARG cc_start: 0.9008 (mtp85) cc_final: 0.8674 (mtp180) REVERT: H 20 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8923 (ttmm) REVERT: H 31 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: H 48 TYR cc_start: 0.9285 (t80) cc_final: 0.8897 (t80) REVERT: H 90 TYR cc_start: 0.9323 (t80) cc_final: 0.8847 (t80) REVERT: I 11 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6355 (t80) REVERT: I 108 MET cc_start: 0.8777 (mmm) cc_final: 0.8426 (mmm) REVERT: L 16 ILE cc_start: 0.9140 (tp) cc_final: 0.8910 (tp) REVERT: L 47 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8134 (mmmm) REVERT: D 16 ASP cc_start: 0.7949 (t0) cc_final: 0.7600 (t0) REVERT: D 39 MET cc_start: 0.9289 (ptm) cc_final: 0.8967 (ptt) REVERT: D 70 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.7854 (ttp-170) REVERT: G 24 ASN cc_start: 0.8787 (t0) cc_final: 0.8572 (t0) REVERT: G 80 PHE cc_start: 0.7498 (m-10) cc_final: 0.6957 (m-10) REVERT: G 86 ASP cc_start: 0.6978 (m-30) cc_final: 0.6137 (m-30) REVERT: G 94 LYS cc_start: 0.6449 (mmpt) cc_final: 0.5508 (pttt) REVERT: G 121 PRO cc_start: 0.6909 (Cg_exo) cc_final: 0.6655 (Cg_exo) REVERT: G 158 PHE cc_start: 0.9029 (m-80) cc_final: 0.8563 (m-80) REVERT: M 247 GLN cc_start: 0.7356 (mp10) cc_final: 0.6092 (pt0) REVERT: M 276 MET cc_start: 0.8064 (mmm) cc_final: 0.7053 (mmm) REVERT: M 309 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7239 (mt-10) REVERT: M 494 TYR cc_start: 0.8096 (t80) cc_final: 0.7629 (t80) outliers start: 82 outliers final: 60 residues processed: 459 average time/residue: 0.2298 time to fit residues: 171.7554 Evaluate side-chains 455 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 383 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 32 optimal weight: 0.1980 chunk 178 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1310 HIS B 525 ASN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.095355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062579 restraints weight = 84721.505| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.15 r_work: 0.2822 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36249 Z= 0.153 Angle : 0.671 12.615 49309 Z= 0.336 Chirality : 0.046 0.280 5510 Planarity : 0.004 0.054 6104 Dihedral : 13.567 168.401 5473 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 2.07 % Allowed : 15.32 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.32 (0.13), residues: 4169 helix: 1.00 (0.14), residues: 1389 sheet: -0.75 (0.21), residues: 576 loop : -0.82 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 109 TYR 0.024 0.001 TYR E 125 PHE 0.022 0.001 PHE G 107 TRP 0.035 0.002 TRP A1210 HIS 0.013 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (36221) covalent geometry : angle 0.66411 / 0.34 (49279) hydrogen bonds : bond 0.03899 / 2.59 ( 1383) hydrogen bonds : angle 4.94339 / 3.56 ( 3834) metal coordination : bond 0.00618 / 0.40 ( 28) metal coordination : angle 3.93996 / 2.86 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 404 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 330 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 905 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8536 (t0) REVERT: A 930 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9089 (tt) REVERT: A 1166 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8950 (tt) REVERT: A 1396 ARG cc_start: 0.8368 (mmt-90) cc_final: 0.8095 (mmt-90) REVERT: A 1439 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9001 (mm) REVERT: B 36 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 668 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (mm) REVERT: B 692 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8830 (p) REVERT: B 954 MET cc_start: 0.9338 (tpp) cc_final: 0.9069 (mmt) REVERT: C 94 CYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7112 (p) REVERT: C 111 GLN cc_start: 0.8250 (mp10) cc_final: 0.8021 (mp10) REVERT: E 90 TYR cc_start: 0.9509 (m-80) cc_final: 0.9242 (m-80) REVERT: E 94 MET cc_start: 0.8435 (mmm) cc_final: 0.8142 (mmm) REVERT: F 100 ARG cc_start: 0.8997 (mtp85) cc_final: 0.8660 (mtp180) REVERT: H 20 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8931 (ttmm) REVERT: H 31 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: H 48 TYR cc_start: 0.9271 (t80) cc_final: 0.8880 (t80) REVERT: H 90 TYR cc_start: 0.9311 (t80) cc_final: 0.8773 (t80) REVERT: I 11 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6300 (t80) REVERT: I 40 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7178 (ptp-170) REVERT: I 47 GLU cc_start: 0.7166 (pp20) cc_final: 0.6724 (pp20) REVERT: I 110 LEU cc_start: 0.9390 (mt) cc_final: 0.9172 (mt) REVERT: L 16 ILE cc_start: 0.9056 (tp) cc_final: 0.8768 (tp) REVERT: L 47 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8174 (mmmm) REVERT: D 16 ASP cc_start: 0.8000 (t0) cc_final: 0.7664 (t0) REVERT: D 33 LEU cc_start: 0.8823 (mm) cc_final: 0.8595 (tp) REVERT: D 39 MET cc_start: 0.9305 (ptm) cc_final: 0.8974 (ptt) REVERT: D 70 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7828 (ttp-170) REVERT: D 84 ARG cc_start: 0.9285 (tpt170) cc_final: 0.9083 (tpt170) REVERT: G 1 MET cc_start: 0.7684 (ppp) cc_final: 0.6508 (ppp) REVERT: G 3 TYR cc_start: 0.7899 (m-80) cc_final: 0.6941 (m-80) REVERT: G 24 ASN cc_start: 0.8735 (t0) cc_final: 0.8526 (t0) REVERT: G 37 THR cc_start: 0.9414 (t) cc_final: 0.9199 (p) REVERT: G 80 PHE cc_start: 0.7569 (m-10) cc_final: 0.5835 (m-10) REVERT: G 86 ASP cc_start: 0.6999 (m-30) cc_final: 0.6056 (m-30) REVERT: G 94 LYS cc_start: 0.6561 (mmpt) cc_final: 0.5634 (pttt) REVERT: G 121 PRO cc_start: 0.6702 (Cg_exo) cc_final: 0.6432 (Cg_exo) REVERT: G 158 PHE cc_start: 0.9078 (m-80) cc_final: 0.8607 (m-80) REVERT: M 247 GLN cc_start: 0.7340 (mp10) cc_final: 0.5973 (pt0) REVERT: M 276 MET cc_start: 0.8068 (mmm) cc_final: 0.7091 (mmm) REVERT: M 309 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7275 (mt-10) REVERT: M 335 MET cc_start: 0.6643 (tpp) cc_final: 0.5884 (ptm) REVERT: M 494 TYR cc_start: 0.8088 (t80) cc_final: 0.7667 (t80) outliers start: 77 outliers final: 53 residues processed: 460 average time/residue: 0.2108 time to fit residues: 158.7137 Evaluate side-chains 454 residues out of total 3741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 389 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 467 VAL Chi-restraints excluded: chain M residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 139 optimal weight: 0.9980 chunk 314 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN I 46 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.094758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.062153 restraints weight = 84316.847| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.13 r_work: 0.2810 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36249 Z= 0.184 Angle : 0.683 13.091 49309 Z= 0.341 Chirality : 0.047 0.280 5510 Planarity : 0.004 0.054 6104 Dihedral : 13.578 167.996 5473 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 1.93 % Allowed : 15.83 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.34 (0.13), residues: 4169 helix: 0.96 (0.14), residues: 1396 sheet: -0.74 (0.21), residues: 574 loop : -0.84 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 109 TYR 0.024 0.002 TYR E 125 PHE 0.023 0.001 PHE B 309 TRP 0.034 0.002 TRP A1210 HIS 0.012 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (36221) covalent geometry : angle 0.67584 / 0.34 (49279) hydrogen bonds : bond 0.03911 / 2.59 ( 1383) hydrogen bonds : angle 4.93937 / 3.56 ( 3834) metal coordination : bond 0.00771 / 0.50 ( 28) metal coordination : angle 3.97323 / 2.94 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8731.23 seconds wall clock time: 150 minutes 33.99 seconds (9033.99 seconds total)