Starting phenix.real_space_refine on Sat Aug 8 21:28:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sb3_54711/08_2026/9sb3_54711.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sb3_54711/08_2026/9sb3_54711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sb3_54711/08_2026/9sb3_54711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sb3_54711/08_2026/9sb3_54711.map" model { file = "/net/cci-nas-00/data/ceres_data/9sb3_54711/08_2026/9sb3_54711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sb3_54711/08_2026/9sb3_54711.cif" } resolution = 3.05 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= 0.048 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 56 5.49 5 Mg 1 5.21 5 S 171 5.16 5 C 18565 2.51 5 N 5188 2.21 5 O 5729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 29718 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 11008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 11008 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1333} Chain breaks: 7 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {' ZN': 1, 'PPV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 457 SG CYS A 67 17.599 70.632 84.358 1.00 97.69 S ATOM 479 SG CYS A 70 17.133 73.877 82.472 1.00 75.02 S ATOM 532 SG CYS A 77 20.598 72.315 82.807 1.00 77.75 S ATOM 762 SG CYS A 107 35.568 80.221 127.493 1.00110.97 S ATOM 786 SG CYS A 110 33.250 83.063 127.074 1.00101.93 S ATOM 1091 SG CYS A 148 36.245 83.309 129.608 1.00105.31 S ATOM 1190 SG CYS A 167 33.111 81.209 130.297 1.00120.67 S ATOM 19782 SG CYS B1163 19.161 86.613 92.128 1.00 75.52 S ATOM 19800 SG CYS B1166 21.788 84.476 93.582 1.00 66.35 S ATOM 19925 SG CYS B1182 18.302 82.975 92.704 1.00 85.50 S ATOM 19944 SG CYS B1185 18.822 85.171 95.759 1.00 91.51 S ATOM 20932 SG CYS C 86 45.266 60.918 20.436 1.00 97.92 S ATOM 20949 SG CYS C 88 43.794 58.486 22.940 1.00 98.37 S ATOM 20982 SG CYS C 92 45.557 57.170 19.914 1.00 84.38 S ATOM 21005 SG CYS C 95 47.564 58.849 22.718 1.00 71.99 S ATOM 25923 SG CYS I 7 95.206 48.955 135.273 1.00138.75 S ATOM 25948 SG CYS I 10 91.682 47.971 134.676 1.00161.59 S ATOM 26114 SG CYS I 29 92.325 51.510 135.925 1.00160.04 S ATOM 26138 SG CYS I 32 92.857 48.599 138.256 1.00132.08 S ATOM 26465 SG CYS I 75 119.959 58.298 97.941 1.00101.18 S ATOM 26487 SG CYS I 78 121.547 54.864 97.469 1.00123.64 S ATOM 26703 SG CYS I 103 117.933 55.387 96.554 1.00111.03 S ATOM 26723 SG CYS I 106 119.058 55.260 100.199 1.00108.56 S ATOM 26842 SG CYS J 7 75.403 59.446 38.439 1.00 38.05 S ATOM 26865 SG CYS J 10 75.549 61.277 35.136 1.00 59.44 S ATOM 27145 SG CYS J 45 78.366 61.697 37.721 1.00 62.74 S ATOM 27151 SG CYS J 46 77.997 58.470 35.774 1.00 57.08 S ATOM 28274 SG CYS L 31 50.045 27.644 55.336 1.00 99.90 S ATOM 28294 SG CYS L 34 50.857 24.805 52.927 1.00105.99 S ATOM 28398 SG CYS L 48 47.457 25.034 54.736 1.00 91.57 S ATOM 28421 SG CYS L 51 50.651 24.088 56.629 1.00114.78 S Time building chain proxies: 5.78, per 1000 atoms: 0.19 Number of scatterers: 29718 At special positions: 0 Unit cell: (134.269, 155.925, 159.173, 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 171 16.00 P 56 15.00 Mg 1 11.99 O 5729 8.00 N 5188 7.00 C 18565 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 41 sheets defined 38.2% alpha, 18.4% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.557A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.650A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.790A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.656A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.902A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.592A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 removed outlier: 3.512A pdb=" N GLU A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.538A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.798A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.624A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.588A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.691A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1175 Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.612A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.898A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.631A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.102A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.486A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.624A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.545A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.660A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.518A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.517A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.752A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.623A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.564A pdb=" N ILE B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.529A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.405A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.807A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 removed outlier: 3.516A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.501A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.234A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.583A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.044A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.931A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.813A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.624A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 91 removed outlier: 11.366A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.873A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.545A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.666A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.894A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.622A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.958A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.878A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.745A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 6.737A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1378 through 1379 removed outlier: 8.412A pdb=" N GLY A1379 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.040A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 134 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.040A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.524A pdb=" N ALA B 214 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.851A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.951A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.313A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.040A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.040A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.041A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.683A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.659A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.973A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.459A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.654A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE4, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.179A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.731A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) 1194 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9449 1.34 - 1.46: 4327 1.46 - 1.58: 16207 1.58 - 1.69: 107 1.69 - 1.81: 275 Bond restraints: 30365 Sorted by residual: bond pdb=" C3' DC T 39 " pdb=" C2' DC T 39 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.18e+00 bond pdb=" C3' DT T 41 " pdb=" C2' DT T 41 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.84e+00 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.25e+00 bond pdb=" C3' DA N 63 " pdb=" C2' DA N 63 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.86e+00 bond pdb=" C3' DC T 22 " pdb=" C2' DC T 22 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.67e+00 ... (remaining 30360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 41078 2.82 - 5.64: 152 5.64 - 8.46: 6 8.46 - 11.28: 1 11.28 - 14.10: 1 Bond angle restraints: 41238 Sorted by residual: angle pdb=" P1 PPV B1301 " pdb=" OPP PPV B1301 " pdb=" P2 PPV B1301 " ideal model delta sigma weight residual 137.40 123.30 14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O4' DC T 35 " pdb=" C4' DC T 35 " pdb=" C3' DC T 35 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT T 27 " pdb=" C4 DT T 27 " pdb=" O4 DT T 27 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT T 36 " pdb=" C4 DT T 36 " pdb=" O4 DT T 36 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT T 25 " pdb=" C4 DT T 25 " pdb=" O4 DT T 25 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 41233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 17922 26.43 - 52.86: 455 52.86 - 79.29: 85 79.29 - 105.73: 5 105.73 - 132.16: 1 Dihedral angle restraints: 18468 sinusoidal: 8034 harmonic: 10434 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU A 997 " pdb=" C LEU A 997 " pdb=" N LEU A 998 " pdb=" CA LEU A 998 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE A 22 " pdb=" C PHE A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 18465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3273 0.037 - 0.075: 915 0.075 - 0.112: 355 0.112 - 0.149: 85 0.149 - 0.187: 2 Chirality restraints: 4630 Sorted by residual: chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE A1436 " pdb=" N ILE A1436 " pdb=" C ILE A1436 " pdb=" CB ILE A1436 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 4627 not shown) Planarity restraints: 5152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1077 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C THR A1077 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A1077 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A1078 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1074 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A1075 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1075 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1075 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C LEU A 710 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.012 2.00e-02 2.50e+03 ... (remaining 5149 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 185 2.54 - 3.13: 22462 3.13 - 3.72: 45834 3.72 - 4.31: 65698 4.31 - 4.90: 110609 Nonbonded interactions: 244788 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 1.955 2.170 nonbonded pdb=" O3' A R 18 " pdb="MG MG A1801 " model vdw 2.006 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1801 " model vdw 2.090 2.170 nonbonded pdb=" O LYS B 801 " pdb=" OG1 THR J 52 " model vdw 2.093 3.040 nonbonded pdb=" OD1 ASN C 54 " pdb=" OG1 THR C 56 " model vdw 2.170 3.040 ... (remaining 244783 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: 2.500 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.002 0.054 30397 Z= 0.168 Angle : 0.518 14.104 41283 Z= 0.318 Chirality : 0.042 0.187 4630 Planarity : 0.003 0.055 5152 Dihedral : 11.827 132.158 11712 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 0.09 % Allowed : 0.06 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3550 helix: 1.75 (0.16), residues: 1180 sheet: 0.24 (0.23), residues: 564 loop : -0.20 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1274 TYR 0.022 0.001 TYR B 797 PHE 0.022 0.001 PHE A 444 TRP 0.017 0.001 TRP A1044 HIS 0.009 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.17 (30365) covalent geometry : angle 0.51177 / 0.32 (41238) hydrogen bonds : bond 0.17551 / 11.76 ( 1244) hydrogen bonds : angle 6.44226 / 4.53 ( 3424) metal coordination : bond 0.00382 / 0.24 ( 32) metal coordination : angle 2.42341 / 1.66 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 781 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8228 (tp30) cc_final: 0.7974 (mm-30) REVERT: A 144 THR cc_start: 0.8215 (p) cc_final: 0.7979 (t) REVERT: A 264 PHE cc_start: 0.8393 (m-10) cc_final: 0.8003 (m-80) REVERT: A 346 ASP cc_start: 0.8779 (m-30) cc_final: 0.8535 (m-30) REVERT: A 360 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 390 GLN cc_start: 0.8148 (tp40) cc_final: 0.7831 (tp40) REVERT: A 513 SER cc_start: 0.8878 (t) cc_final: 0.8411 (p) REVERT: A 521 MET cc_start: 0.8871 (mtt) cc_final: 0.8649 (mtp) REVERT: A 676 MET cc_start: 0.8491 (mmm) cc_final: 0.8244 (mmm) REVERT: A 695 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8237 (mtmt) REVERT: A 907 THR cc_start: 0.7534 (p) cc_final: 0.7327 (t) REVERT: A 948 VAL cc_start: 0.8809 (t) cc_final: 0.8551 (m) REVERT: A 1013 ASP cc_start: 0.8038 (m-30) cc_final: 0.7804 (m-30) REVERT: A 1135 ARG cc_start: 0.7923 (tmt170) cc_final: 0.7170 (tmm160) REVERT: A 1151 GLU cc_start: 0.7838 (pm20) cc_final: 0.7603 (pt0) REVERT: A 1225 PHE cc_start: 0.7835 (t80) cc_final: 0.7340 (t80) REVERT: A 1230 GLU cc_start: 0.5368 (mm-30) cc_final: 0.4696 (tt0) REVERT: A 1301 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6859 (tm-30) REVERT: A 1393 ASN cc_start: 0.8240 (p0) cc_final: 0.7777 (p0) REVERT: A 1411 GLU cc_start: 0.8230 (tp30) cc_final: 0.7820 (mm-30) REVERT: A 1419 ASP cc_start: 0.8549 (t0) cc_final: 0.8329 (t0) REVERT: B 26 THR cc_start: 0.8829 (p) cc_final: 0.8424 (t) REVERT: B 134 LYS cc_start: 0.6916 (tptp) cc_final: 0.6248 (mttp) REVERT: B 280 ILE cc_start: 0.8945 (mp) cc_final: 0.8659 (mt) REVERT: B 337 ARG cc_start: 0.6356 (mmt180) cc_final: 0.5929 (mmp-170) REVERT: B 391 ASP cc_start: 0.8370 (m-30) cc_final: 0.8144 (m-30) REVERT: B 422 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7492 (mmmt) REVERT: B 444 MET cc_start: 0.7175 (mmp) cc_final: 0.6515 (pmm) REVERT: B 542 MET cc_start: 0.8862 (mtm) cc_final: 0.8598 (mtt) REVERT: B 667 GLN cc_start: 0.6324 (tt0) cc_final: 0.6071 (pp30) REVERT: B 875 GLU cc_start: 0.7964 (pt0) cc_final: 0.7372 (tt0) REVERT: B 885 MET cc_start: 0.6610 (mmm) cc_final: 0.6276 (mmt) REVERT: B 906 SER cc_start: 0.8465 (p) cc_final: 0.8160 (m) REVERT: B 957 ASN cc_start: 0.7404 (t0) cc_final: 0.6925 (t0) REVERT: B 1150 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8167 (mmp-170) REVERT: B 1223 ASP cc_start: 0.7375 (t0) cc_final: 0.7062 (p0) REVERT: C 134 ILE cc_start: 0.8924 (mm) cc_final: 0.8718 (mm) REVERT: E 3 GLN cc_start: 0.6731 (mt0) cc_final: 0.5415 (tp-100) REVERT: E 94 LYS cc_start: 0.7504 (mmmt) cc_final: 0.7242 (mmmt) REVERT: E 97 VAL cc_start: 0.8119 (t) cc_final: 0.7580 (p) REVERT: F 127 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8087 (mt-10) REVERT: H 8 ASP cc_start: 0.7897 (t0) cc_final: 0.7537 (t0) REVERT: H 37 LYS cc_start: 0.8505 (ptpt) cc_final: 0.8000 (ptmm) REVERT: H 53 ASP cc_start: 0.8357 (m-30) cc_final: 0.8034 (m-30) REVERT: H 138 GLU cc_start: 0.7616 (pt0) cc_final: 0.7095 (pm20) REVERT: I 70 ARG cc_start: 0.8555 (mtt90) cc_final: 0.8349 (mtm-85) REVERT: K 88 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7918 (mttp) outliers start: 3 outliers final: 2 residues processed: 784 average time/residue: 0.2256 time to fit residues: 268.1352 Evaluate side-chains 445 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 443 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 1081 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.4980 overall best weight: 2.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 118 HIS A 299 HIS A 358 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1203 ASN B 60 GLN B 121 ASN B 862 GLN B 887 HIS B 984 HIS I 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107981 restraints weight = 41296.315| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.13 r_work: 0.3252 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30397 Z= 0.181 Angle : 0.585 10.378 41283 Z= 0.307 Chirality : 0.045 0.284 4630 Planarity : 0.005 0.051 5152 Dihedral : 12.111 132.969 4536 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 1.23 % Allowed : 7.41 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3550 helix: 1.44 (0.15), residues: 1212 sheet: 0.12 (0.22), residues: 549 loop : -0.36 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 169 TYR 0.021 0.002 TYR B 797 PHE 0.029 0.002 PHE B 963 TRP 0.014 0.001 TRP A1044 HIS 0.005 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (30365) covalent geometry : angle 0.57549 / 0.31 (41238) hydrogen bonds : bond 0.05021 / 3.48 ( 1244) hydrogen bonds : angle 4.95266 / 3.53 ( 3424) metal coordination : bond 0.00561 / 0.30 ( 32) metal coordination : angle 3.28092 / 2.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 456 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.5291 (mmtt) cc_final: 0.5027 (mmmt) REVERT: A 76 GLU cc_start: 0.8428 (tp30) cc_final: 0.8150 (mm-30) REVERT: A 144 THR cc_start: 0.8371 (p) cc_final: 0.8147 (t) REVERT: A 264 PHE cc_start: 0.8443 (m-10) cc_final: 0.8166 (m-10) REVERT: A 390 GLN cc_start: 0.8292 (tp40) cc_final: 0.7883 (tp40) REVERT: A 513 SER cc_start: 0.8958 (t) cc_final: 0.8448 (p) REVERT: A 521 MET cc_start: 0.8983 (mtt) cc_final: 0.8738 (mtp) REVERT: A 695 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8075 (mtmt) REVERT: A 948 VAL cc_start: 0.8798 (t) cc_final: 0.8576 (m) REVERT: A 1013 ASP cc_start: 0.8118 (m-30) cc_final: 0.7811 (m-30) REVERT: A 1063 MET cc_start: 0.8889 (mmm) cc_final: 0.8675 (mmt) REVERT: A 1121 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 1135 ARG cc_start: 0.7793 (tmt170) cc_final: 0.7012 (tmm160) REVERT: A 1159 ARG cc_start: 0.6770 (tpp80) cc_final: 0.5630 (mpt180) REVERT: A 1199 ARG cc_start: 0.7371 (tmt170) cc_final: 0.7046 (tpt-90) REVERT: A 1230 GLU cc_start: 0.5706 (mm-30) cc_final: 0.4794 (tt0) REVERT: A 1300 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7180 (mttp) REVERT: A 1393 ASN cc_start: 0.8444 (p0) cc_final: 0.7947 (p0) REVERT: A 1398 MET cc_start: 0.8768 (ttm) cc_final: 0.8567 (ttp) REVERT: A 1411 GLU cc_start: 0.8258 (tp30) cc_final: 0.7747 (mm-30) REVERT: B 26 THR cc_start: 0.8794 (p) cc_final: 0.8464 (t) REVERT: B 134 LYS cc_start: 0.7064 (tptp) cc_final: 0.6377 (mttm) REVERT: B 138 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6443 (pt0) REVERT: B 393 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7783 (mtpt) REVERT: B 422 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7412 (mmmt) REVERT: B 444 MET cc_start: 0.7346 (mmp) cc_final: 0.6320 (pmm) REVERT: B 498 THR cc_start: 0.8439 (m) cc_final: 0.8236 (p) REVERT: B 542 MET cc_start: 0.9068 (mtm) cc_final: 0.8748 (mtt) REVERT: B 595 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6787 (mtm-85) REVERT: B 875 GLU cc_start: 0.8047 (pt0) cc_final: 0.7416 (tt0) REVERT: B 906 SER cc_start: 0.8539 (p) cc_final: 0.8222 (m) REVERT: B 1223 ASP cc_start: 0.7478 (t0) cc_final: 0.7116 (p0) REVERT: E 3 GLN cc_start: 0.6771 (mt0) cc_final: 0.5331 (tp-100) REVERT: E 94 LYS cc_start: 0.7526 (mmmt) cc_final: 0.7197 (mmmt) REVERT: E 97 VAL cc_start: 0.8023 (t) cc_final: 0.7822 (m) REVERT: F 103 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: F 149 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: H 37 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7577 (ptmm) REVERT: H 138 GLU cc_start: 0.7700 (pt0) cc_final: 0.6995 (pm20) REVERT: I 17 ARG cc_start: 0.6410 (tmm-80) cc_final: 0.6090 (tmm-80) REVERT: K 88 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7854 (mttp) REVERT: L 44 ASP cc_start: 0.6435 (t0) cc_final: 0.5929 (t0) outliers start: 39 outliers final: 27 residues processed: 480 average time/residue: 0.2056 time to fit residues: 153.8584 Evaluate side-chains 431 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 401 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 17 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 272 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 303 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 148 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN B 224 GLN I 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107967 restraints weight = 41608.609| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.18 r_work: 0.3243 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30397 Z= 0.144 Angle : 0.529 10.579 41283 Z= 0.277 Chirality : 0.043 0.268 4630 Planarity : 0.004 0.051 5152 Dihedral : 12.115 133.145 4536 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.58 % Allowed : 8.90 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3550 helix: 1.44 (0.15), residues: 1218 sheet: 0.08 (0.22), residues: 555 loop : -0.39 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.015 0.001 TYR B 811 PHE 0.030 0.001 PHE A 444 TRP 0.013 0.001 TRP A1044 HIS 0.006 0.001 HIS A 906 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (30365) covalent geometry : angle 0.52038 / 0.28 (41238) hydrogen bonds : bond 0.04447 / 3.10 ( 1244) hydrogen bonds : angle 4.64745 / 3.32 ( 3424) metal coordination : bond 0.00427 / 0.24 ( 32) metal coordination : angle 2.87473 / 1.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 433 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 49 LYS cc_start: 0.5270 (mmtt) cc_final: 0.4941 (mmmt) REVERT: A 76 GLU cc_start: 0.8432 (tp30) cc_final: 0.8173 (mm-30) REVERT: A 144 THR cc_start: 0.8396 (p) cc_final: 0.8194 (t) REVERT: A 390 GLN cc_start: 0.8273 (tp40) cc_final: 0.7878 (tp40) REVERT: A 513 SER cc_start: 0.8970 (t) cc_final: 0.8505 (p) REVERT: A 618 GLU cc_start: 0.8226 (pm20) cc_final: 0.7970 (pm20) REVERT: A 695 LYS cc_start: 0.8393 (mmtm) cc_final: 0.8100 (mtmt) REVERT: A 895 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8135 (tttp) REVERT: A 948 VAL cc_start: 0.8770 (t) cc_final: 0.8567 (m) REVERT: A 1013 ASP cc_start: 0.8104 (m-30) cc_final: 0.7822 (m-30) REVERT: A 1063 MET cc_start: 0.8870 (mmm) cc_final: 0.8649 (mmt) REVERT: A 1121 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 1135 ARG cc_start: 0.7865 (tmt170) cc_final: 0.7043 (tmm160) REVERT: A 1159 ARG cc_start: 0.7086 (tpp80) cc_final: 0.5926 (mpt180) REVERT: A 1199 ARG cc_start: 0.7312 (tmt170) cc_final: 0.7072 (tmt170) REVERT: A 1230 GLU cc_start: 0.5503 (mm-30) cc_final: 0.4701 (tt0) REVERT: A 1301 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 1393 ASN cc_start: 0.8354 (p0) cc_final: 0.7860 (p0) REVERT: A 1411 GLU cc_start: 0.8309 (tp30) cc_final: 0.7788 (mm-30) REVERT: B 26 THR cc_start: 0.8764 (p) cc_final: 0.8429 (t) REVERT: B 134 LYS cc_start: 0.6985 (tptp) cc_final: 0.6340 (mttm) REVERT: B 138 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6424 (pt0) REVERT: B 444 MET cc_start: 0.7361 (mmp) cc_final: 0.6333 (pmm) REVERT: B 531 GLN cc_start: 0.6642 (mm-40) cc_final: 0.6111 (tp40) REVERT: B 542 MET cc_start: 0.9092 (mtm) cc_final: 0.8782 (mtt) REVERT: B 595 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6840 (mtm-85) REVERT: B 875 GLU cc_start: 0.8068 (pt0) cc_final: 0.7449 (tt0) REVERT: B 906 SER cc_start: 0.8548 (p) cc_final: 0.8210 (m) REVERT: B 1223 ASP cc_start: 0.7534 (t0) cc_final: 0.7160 (p0) REVERT: E 3 GLN cc_start: 0.6668 (mt0) cc_final: 0.5293 (tp-100) REVERT: E 94 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7178 (mmmt) REVERT: H 37 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7594 (ptmm) REVERT: H 53 ASP cc_start: 0.8422 (m-30) cc_final: 0.7998 (m-30) REVERT: H 138 GLU cc_start: 0.7772 (pt0) cc_final: 0.7083 (pm20) REVERT: I 17 ARG cc_start: 0.6568 (tmm-80) cc_final: 0.6216 (tmm-80) REVERT: J 26 GLN cc_start: 0.8708 (mt0) cc_final: 0.8477 (mp10) REVERT: K 24 ASP cc_start: 0.8426 (t0) cc_final: 0.8219 (t0) REVERT: K 31 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8667 (m) REVERT: K 88 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7858 (mttp) REVERT: L 44 ASP cc_start: 0.6468 (t0) cc_final: 0.6014 (t0) outliers start: 50 outliers final: 33 residues processed: 461 average time/residue: 0.2046 time to fit residues: 148.3904 Evaluate side-chains 440 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 405 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 28 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.0060 chunk 48 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN B 395 GLN E 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105389 restraints weight = 41209.698| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.15 r_work: 0.3209 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30397 Z= 0.169 Angle : 0.545 9.291 41283 Z= 0.286 Chirality : 0.044 0.268 4630 Planarity : 0.004 0.051 5152 Dihedral : 12.159 133.646 4536 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 1.61 % Allowed : 10.19 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3550 helix: 1.34 (0.15), residues: 1225 sheet: -0.04 (0.22), residues: 573 loop : -0.43 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.016 0.002 TYR B 811 PHE 0.026 0.002 PHE A 219 TRP 0.012 0.001 TRP A1228 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (30365) covalent geometry : angle 0.53560 / 0.29 (41238) hydrogen bonds : bond 0.04278 / 3.01 ( 1244) hydrogen bonds : angle 4.51319 / 3.23 ( 3424) metal coordination : bond 0.00500 / 0.30 ( 32) metal coordination : angle 3.06984 / 1.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 431 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 49 LYS cc_start: 0.5278 (mmtt) cc_final: 0.4702 (mmmt) REVERT: A 76 GLU cc_start: 0.8430 (tp30) cc_final: 0.8184 (mm-30) REVERT: A 144 THR cc_start: 0.8504 (p) cc_final: 0.8299 (t) REVERT: A 390 GLN cc_start: 0.8322 (tp40) cc_final: 0.7913 (tp40) REVERT: A 513 SER cc_start: 0.9004 (t) cc_final: 0.8497 (p) REVERT: A 695 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8125 (mtmt) REVERT: A 895 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7825 (ttmt) REVERT: A 948 VAL cc_start: 0.8818 (t) cc_final: 0.8617 (m) REVERT: A 978 PRO cc_start: 0.8187 (Cg_exo) cc_final: 0.7803 (Cg_endo) REVERT: A 1013 ASP cc_start: 0.8136 (m-30) cc_final: 0.7842 (m-30) REVERT: A 1063 MET cc_start: 0.8858 (mmm) cc_final: 0.8630 (mmt) REVERT: A 1121 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 1135 ARG cc_start: 0.7817 (tmt170) cc_final: 0.6968 (tmm160) REVERT: A 1159 ARG cc_start: 0.7027 (tpp80) cc_final: 0.5944 (mpt180) REVERT: A 1199 ARG cc_start: 0.7353 (tmt170) cc_final: 0.7134 (tpt-90) REVERT: A 1225 PHE cc_start: 0.7411 (t80) cc_final: 0.7109 (t80) REVERT: A 1230 GLU cc_start: 0.5436 (mm-30) cc_final: 0.4579 (tt0) REVERT: A 1393 ASN cc_start: 0.8378 (p0) cc_final: 0.7881 (p0) REVERT: A 1411 GLU cc_start: 0.8326 (tp30) cc_final: 0.7822 (mm-30) REVERT: B 26 THR cc_start: 0.8863 (p) cc_final: 0.8524 (t) REVERT: B 134 LYS cc_start: 0.7000 (tptp) cc_final: 0.6293 (mttm) REVERT: B 138 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6248 (pt0) REVERT: B 444 MET cc_start: 0.7357 (mmp) cc_final: 0.6320 (pmm) REVERT: B 531 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6165 (tp40) REVERT: B 542 MET cc_start: 0.9177 (mtm) cc_final: 0.8891 (mtt) REVERT: B 561 TRP cc_start: 0.6710 (m-10) cc_final: 0.6434 (m-10) REVERT: B 875 GLU cc_start: 0.8130 (pt0) cc_final: 0.7414 (tt0) REVERT: B 906 SER cc_start: 0.8485 (p) cc_final: 0.8131 (m) REVERT: B 1223 ASP cc_start: 0.7546 (t0) cc_final: 0.7261 (p0) REVERT: E 3 GLN cc_start: 0.6691 (mt0) cc_final: 0.5327 (tp-100) REVERT: H 8 ASP cc_start: 0.7930 (t0) cc_final: 0.7498 (t0) REVERT: H 37 LYS cc_start: 0.8312 (ptpt) cc_final: 0.7802 (ptmm) REVERT: H 53 ASP cc_start: 0.8353 (m-30) cc_final: 0.7934 (m-30) REVERT: H 138 GLU cc_start: 0.7744 (pt0) cc_final: 0.7043 (pm20) REVERT: I 13 MET cc_start: 0.7822 (ttp) cc_final: 0.7560 (ttp) REVERT: I 17 ARG cc_start: 0.6562 (tmm-80) cc_final: 0.6180 (tmm-80) REVERT: J 1 MET cc_start: 0.7830 (mtt) cc_final: 0.7028 (mmt) REVERT: K 24 ASP cc_start: 0.8524 (t0) cc_final: 0.8194 (t0) REVERT: K 31 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8740 (m) REVERT: K 88 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7852 (mttp) REVERT: L 44 ASP cc_start: 0.6399 (t0) cc_final: 0.5852 (t0) outliers start: 51 outliers final: 34 residues processed: 462 average time/residue: 0.2034 time to fit residues: 148.5036 Evaluate side-chains 430 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 394 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 244 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 348 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 146 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 HIS A 975 HIS A1078 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106960 restraints weight = 41163.449| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30397 Z= 0.121 Angle : 0.504 8.544 41283 Z= 0.265 Chirality : 0.042 0.269 4630 Planarity : 0.004 0.051 5152 Dihedral : 12.124 133.887 4536 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.42 % Allowed : 11.27 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3550 helix: 1.52 (0.15), residues: 1213 sheet: 0.02 (0.22), residues: 565 loop : -0.42 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.015 0.001 TYR H 129 PHE 0.026 0.001 PHE A 444 TRP 0.013 0.001 TRP A1044 HIS 0.004 0.001 HIS A 906 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30365) covalent geometry : angle 0.49600 / 0.26 (41238) hydrogen bonds : bond 0.03941 / 2.78 ( 1244) hydrogen bonds : angle 4.36430 / 3.13 ( 3424) metal coordination : bond 0.00371 / 0.21 ( 32) metal coordination : angle 2.83350 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 426 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 GLN cc_start: 0.8271 (tp40) cc_final: 0.7817 (tp40) REVERT: A 513 SER cc_start: 0.9111 (t) cc_final: 0.8622 (p) REVERT: A 618 GLU cc_start: 0.8206 (pm20) cc_final: 0.7948 (pm20) REVERT: A 695 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8110 (mtmt) REVERT: A 830 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.4549 (pmtt) REVERT: A 978 PRO cc_start: 0.8227 (Cg_exo) cc_final: 0.7858 (Cg_endo) REVERT: A 1063 MET cc_start: 0.8848 (mmm) cc_final: 0.8616 (mmt) REVERT: A 1081 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.4870 (tm) REVERT: A 1121 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 1135 ARG cc_start: 0.7896 (tmt170) cc_final: 0.7086 (tmm160) REVERT: A 1159 ARG cc_start: 0.7039 (tpp80) cc_final: 0.5958 (mpt180) REVERT: A 1199 ARG cc_start: 0.7386 (tmt170) cc_final: 0.7122 (tpt-90) REVERT: A 1225 PHE cc_start: 0.7387 (t80) cc_final: 0.7052 (t80) REVERT: A 1230 GLU cc_start: 0.5502 (mm-30) cc_final: 0.4634 (tt0) REVERT: A 1281 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8010 (ttp-110) REVERT: A 1393 ASN cc_start: 0.8344 (p0) cc_final: 0.8106 (p0) REVERT: A 1411 GLU cc_start: 0.8250 (tp30) cc_final: 0.7757 (mm-30) REVERT: B 26 THR cc_start: 0.8838 (p) cc_final: 0.8512 (t) REVERT: B 134 LYS cc_start: 0.6916 (tptp) cc_final: 0.6187 (mttm) REVERT: B 138 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6283 (pt0) REVERT: B 259 TYR cc_start: 0.7216 (m-80) cc_final: 0.6976 (m-80) REVERT: B 270 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7937 (mtmm) REVERT: B 444 MET cc_start: 0.7361 (mmp) cc_final: 0.6283 (pmm) REVERT: B 531 GLN cc_start: 0.6730 (mm-40) cc_final: 0.6216 (tp40) REVERT: B 542 MET cc_start: 0.9184 (mtm) cc_final: 0.8900 (mtt) REVERT: B 561 TRP cc_start: 0.6871 (m-10) cc_final: 0.6430 (m100) REVERT: B 875 GLU cc_start: 0.8044 (pt0) cc_final: 0.7304 (tt0) REVERT: B 906 SER cc_start: 0.8459 (p) cc_final: 0.8112 (m) REVERT: B 1223 ASP cc_start: 0.7446 (t0) cc_final: 0.7207 (p0) REVERT: E 3 GLN cc_start: 0.6549 (mt0) cc_final: 0.5439 (tp-100) REVERT: E 121 MET cc_start: 0.7511 (tpt) cc_final: 0.7295 (tpt) REVERT: E 164 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8236 (tp) REVERT: H 8 ASP cc_start: 0.7885 (t0) cc_final: 0.7492 (t0) REVERT: H 37 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7770 (ptmm) REVERT: H 53 ASP cc_start: 0.8374 (m-30) cc_final: 0.7952 (m-30) REVERT: H 138 GLU cc_start: 0.7721 (pt0) cc_final: 0.7034 (pm20) REVERT: I 17 ARG cc_start: 0.6656 (tmm-80) cc_final: 0.6286 (tmm-80) REVERT: J 1 MET cc_start: 0.7816 (mtt) cc_final: 0.7041 (mmt) REVERT: K 88 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7826 (mttp) REVERT: L 44 ASP cc_start: 0.6430 (t0) cc_final: 0.6061 (t0) outliers start: 45 outliers final: 31 residues processed: 453 average time/residue: 0.1970 time to fit residues: 142.0222 Evaluate side-chains 427 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 393 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 332 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105917 restraints weight = 41635.529| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.19 r_work: 0.3214 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30397 Z= 0.132 Angle : 0.505 8.323 41283 Z= 0.265 Chirality : 0.042 0.268 4630 Planarity : 0.004 0.051 5152 Dihedral : 12.121 133.644 4536 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 1.55 % Allowed : 11.93 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3550 helix: 1.51 (0.15), residues: 1214 sheet: 0.01 (0.22), residues: 562 loop : -0.42 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.016 0.001 TYR H 129 PHE 0.026 0.001 PHE A 444 TRP 0.012 0.001 TRP A1044 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (30365) covalent geometry : angle 0.49719 / 0.27 (41238) hydrogen bonds : bond 0.03925 / 2.77 ( 1244) hydrogen bonds : angle 4.33113 / 3.11 ( 3424) metal coordination : bond 0.00388 / 0.23 ( 32) metal coordination : angle 2.74762 / 1.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 405 time to evaluate : 1.126 Fit side-chains REVERT: A 389 THR cc_start: 0.7676 (m) cc_final: 0.7447 (p) REVERT: A 390 GLN cc_start: 0.8363 (tp40) cc_final: 0.7926 (tp40) REVERT: A 513 SER cc_start: 0.9111 (t) cc_final: 0.8611 (p) REVERT: A 618 GLU cc_start: 0.8146 (pm20) cc_final: 0.7895 (pm20) REVERT: A 695 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8115 (mtmt) REVERT: A 724 GLU cc_start: 0.8106 (tp30) cc_final: 0.7789 (tp30) REVERT: A 830 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.4587 (pmtt) REVERT: A 895 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7843 (ttmt) REVERT: A 978 PRO cc_start: 0.8279 (Cg_exo) cc_final: 0.7951 (Cg_endo) REVERT: A 1013 ASP cc_start: 0.8357 (m-30) cc_final: 0.8088 (m-30) REVERT: A 1063 MET cc_start: 0.8843 (mmm) cc_final: 0.8611 (mmt) REVERT: A 1081 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5002 (tm) REVERT: A 1121 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 1135 ARG cc_start: 0.7899 (tmt170) cc_final: 0.7089 (tmm160) REVERT: A 1159 ARG cc_start: 0.7070 (tpp80) cc_final: 0.5960 (mpt180) REVERT: A 1225 PHE cc_start: 0.7413 (t80) cc_final: 0.7056 (t80) REVERT: A 1230 GLU cc_start: 0.5606 (mm-30) cc_final: 0.4711 (tt0) REVERT: A 1393 ASN cc_start: 0.8372 (p0) cc_final: 0.8130 (p0) REVERT: A 1411 GLU cc_start: 0.8266 (tp30) cc_final: 0.7762 (mm-30) REVERT: B 26 THR cc_start: 0.8874 (p) cc_final: 0.8536 (t) REVERT: B 134 LYS cc_start: 0.6929 (tptp) cc_final: 0.6179 (mttm) REVERT: B 138 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6282 (pt0) REVERT: B 270 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7963 (mtmm) REVERT: B 444 MET cc_start: 0.7372 (mmp) cc_final: 0.6367 (pmm) REVERT: B 531 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6325 (tp40) REVERT: B 542 MET cc_start: 0.9208 (mtm) cc_final: 0.8926 (mtt) REVERT: B 561 TRP cc_start: 0.6856 (m-10) cc_final: 0.6473 (m100) REVERT: B 641 GLU cc_start: 0.7898 (pp20) cc_final: 0.7401 (pp20) REVERT: B 875 GLU cc_start: 0.8032 (pt0) cc_final: 0.7285 (tt0) REVERT: B 906 SER cc_start: 0.8473 (p) cc_final: 0.8135 (m) REVERT: B 1223 ASP cc_start: 0.7492 (t0) cc_final: 0.7230 (p0) REVERT: E 3 GLN cc_start: 0.6553 (mt0) cc_final: 0.5369 (tp-100) REVERT: E 45 LYS cc_start: 0.6985 (tttm) cc_final: 0.6481 (tttm) REVERT: E 121 MET cc_start: 0.7597 (tpt) cc_final: 0.7382 (tpt) REVERT: E 164 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8236 (tp) REVERT: F 114 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6467 (mm-30) REVERT: H 8 ASP cc_start: 0.7907 (t0) cc_final: 0.7526 (t0) REVERT: H 37 LYS cc_start: 0.8320 (ptpt) cc_final: 0.7794 (ptmm) REVERT: H 53 ASP cc_start: 0.8394 (m-30) cc_final: 0.7959 (m-30) REVERT: H 138 GLU cc_start: 0.7775 (pt0) cc_final: 0.7064 (pm20) REVERT: I 17 ARG cc_start: 0.6637 (tmm-80) cc_final: 0.6229 (tmm-80) REVERT: J 1 MET cc_start: 0.7898 (mtt) cc_final: 0.7216 (mmt) REVERT: K 88 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7812 (mttp) REVERT: L 44 ASP cc_start: 0.6443 (t0) cc_final: 0.6224 (t0) outliers start: 49 outliers final: 35 residues processed: 439 average time/residue: 0.1937 time to fit residues: 134.3351 Evaluate side-chains 429 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 390 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 188 optimal weight: 6.9990 chunk 210 optimal weight: 0.0970 chunk 266 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 GLN J 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104123 restraints weight = 41238.984| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.09 r_work: 0.3188 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30397 Z= 0.168 Angle : 0.539 8.149 41283 Z= 0.283 Chirality : 0.043 0.266 4630 Planarity : 0.004 0.051 5152 Dihedral : 12.149 133.779 4536 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 1.90 % Allowed : 11.87 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3550 helix: 1.43 (0.15), residues: 1214 sheet: -0.01 (0.22), residues: 561 loop : -0.46 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.017 0.001 TYR H 129 PHE 0.026 0.002 PHE B 963 TRP 0.011 0.001 TRP A1044 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (30365) covalent geometry : angle 0.52992 / 0.28 (41238) hydrogen bonds : bond 0.04143 / 2.91 ( 1244) hydrogen bonds : angle 4.38058 / 3.15 ( 3424) metal coordination : bond 0.00500 / 0.31 ( 32) metal coordination : angle 2.98200 / 1.89 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 402 time to evaluate : 1.006 Fit side-chains REVERT: A 390 GLN cc_start: 0.8342 (tp40) cc_final: 0.7922 (tp40) REVERT: A 513 SER cc_start: 0.9088 (t) cc_final: 0.8587 (p) REVERT: A 618 GLU cc_start: 0.8083 (pm20) cc_final: 0.7853 (pm20) REVERT: A 695 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8102 (mtmt) REVERT: A 724 GLU cc_start: 0.8108 (tp30) cc_final: 0.7794 (tp30) REVERT: A 830 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.4512 (pmtt) REVERT: A 895 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8207 (tttp) REVERT: A 978 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8060 (Cg_endo) REVERT: A 1063 MET cc_start: 0.8908 (mmm) cc_final: 0.8676 (mmt) REVERT: A 1081 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.4669 (tm) REVERT: A 1121 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 1135 ARG cc_start: 0.7949 (tmt170) cc_final: 0.7097 (tmm160) REVERT: A 1159 ARG cc_start: 0.7066 (tpp80) cc_final: 0.5945 (mpt180) REVERT: A 1230 GLU cc_start: 0.5569 (mm-30) cc_final: 0.4669 (tt0) REVERT: A 1411 GLU cc_start: 0.8253 (tp30) cc_final: 0.7738 (mm-30) REVERT: B 26 THR cc_start: 0.8917 (p) cc_final: 0.8581 (t) REVERT: B 134 LYS cc_start: 0.6913 (tptp) cc_final: 0.6164 (mttt) REVERT: B 138 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6199 (pt0) REVERT: B 241 ARG cc_start: 0.7273 (mtm180) cc_final: 0.7073 (mtm180) REVERT: B 259 TYR cc_start: 0.7359 (m-80) cc_final: 0.7102 (m-80) REVERT: B 270 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7909 (mtmm) REVERT: B 444 MET cc_start: 0.7198 (mmp) cc_final: 0.6249 (pmm) REVERT: B 531 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6397 (tp40) REVERT: B 542 MET cc_start: 0.9247 (mtm) cc_final: 0.8985 (mtt) REVERT: B 561 TRP cc_start: 0.6760 (m-10) cc_final: 0.6484 (m100) REVERT: B 641 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: B 875 GLU cc_start: 0.8076 (pt0) cc_final: 0.7433 (tt0) REVERT: B 906 SER cc_start: 0.8499 (p) cc_final: 0.8224 (m) REVERT: B 1223 ASP cc_start: 0.7510 (t0) cc_final: 0.7205 (p0) REVERT: E 3 GLN cc_start: 0.6515 (mt0) cc_final: 0.5240 (tp-100) REVERT: E 121 MET cc_start: 0.7597 (tpt) cc_final: 0.7393 (tpt) REVERT: E 164 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8210 (tp) REVERT: F 72 LYS cc_start: 0.7232 (mmtt) cc_final: 0.5888 (mptt) REVERT: F 114 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6561 (mm-30) REVERT: F 127 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8116 (mt-10) REVERT: H 8 ASP cc_start: 0.7922 (t0) cc_final: 0.7530 (t0) REVERT: H 37 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7831 (ptmm) REVERT: H 53 ASP cc_start: 0.8421 (m-30) cc_final: 0.7956 (m-30) REVERT: I 17 ARG cc_start: 0.6554 (tmm-80) cc_final: 0.6132 (tmm-80) REVERT: J 1 MET cc_start: 0.7953 (mtt) cc_final: 0.7326 (mmt) REVERT: J 26 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: K 88 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7805 (mttp) REVERT: L 44 ASP cc_start: 0.6443 (t0) cc_final: 0.6202 (t0) outliers start: 60 outliers final: 42 residues processed: 444 average time/residue: 0.1993 time to fit residues: 139.6330 Evaluate side-chains 427 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 379 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 323 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104026 restraints weight = 41255.379| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.10 r_work: 0.3195 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30397 Z= 0.141 Angle : 0.520 11.410 41283 Z= 0.274 Chirality : 0.043 0.266 4630 Planarity : 0.004 0.055 5152 Dihedral : 12.120 134.147 4536 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.84 % Allowed : 12.66 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3550 helix: 1.45 (0.15), residues: 1210 sheet: -0.02 (0.22), residues: 561 loop : -0.44 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1366 TYR 0.017 0.001 TYR H 129 PHE 0.025 0.001 PHE A 444 TRP 0.012 0.001 TRP A1191 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (30365) covalent geometry : angle 0.51215 / 0.27 (41238) hydrogen bonds : bond 0.03988 / 2.81 ( 1244) hydrogen bonds : angle 4.33284 / 3.12 ( 3424) metal coordination : bond 0.00400 / 0.24 ( 32) metal coordination : angle 2.78032 / 1.80 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 1.049 Fit side-chains REVERT: A 132 LYS cc_start: 0.8128 (mttt) cc_final: 0.7854 (mmtm) REVERT: A 390 GLN cc_start: 0.8360 (tp40) cc_final: 0.7920 (tp40) REVERT: A 513 SER cc_start: 0.9084 (t) cc_final: 0.8588 (p) REVERT: A 695 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8070 (mtmt) REVERT: A 724 GLU cc_start: 0.8125 (tp30) cc_final: 0.7793 (tp30) REVERT: A 830 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.4512 (pmtt) REVERT: A 895 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (tttp) REVERT: A 978 PRO cc_start: 0.8363 (Cg_exo) cc_final: 0.8056 (Cg_endo) REVERT: A 1063 MET cc_start: 0.8867 (mmm) cc_final: 0.8642 (mmt) REVERT: A 1081 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.4618 (tm) REVERT: A 1121 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 1135 ARG cc_start: 0.7899 (tmt170) cc_final: 0.7066 (tmm160) REVERT: A 1159 ARG cc_start: 0.7067 (tpp80) cc_final: 0.5980 (mpt180) REVERT: A 1199 ARG cc_start: 0.6967 (ttt-90) cc_final: 0.6556 (tpt-90) REVERT: A 1230 GLU cc_start: 0.5548 (mm-30) cc_final: 0.4611 (tt0) REVERT: A 1411 GLU cc_start: 0.8211 (tp30) cc_final: 0.7692 (mm-30) REVERT: A 1454 MET cc_start: 0.5581 (ttp) cc_final: 0.5164 (tmm) REVERT: B 26 THR cc_start: 0.8928 (p) cc_final: 0.8592 (t) REVERT: B 134 LYS cc_start: 0.6766 (tptp) cc_final: 0.6141 (mttt) REVERT: B 138 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6199 (pt0) REVERT: B 259 TYR cc_start: 0.7373 (m-80) cc_final: 0.7125 (m-80) REVERT: B 270 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7827 (mttp) REVERT: B 313 MET cc_start: 0.8317 (mtp) cc_final: 0.8050 (mtt) REVERT: B 444 MET cc_start: 0.7019 (mmp) cc_final: 0.6366 (pmm) REVERT: B 531 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6373 (tp40) REVERT: B 561 TRP cc_start: 0.6727 (m-10) cc_final: 0.6479 (m100) REVERT: B 641 GLU cc_start: 0.7958 (pp20) cc_final: 0.7475 (pp20) REVERT: B 875 GLU cc_start: 0.8060 (pt0) cc_final: 0.7418 (tt0) REVERT: B 906 SER cc_start: 0.8482 (p) cc_final: 0.8210 (m) REVERT: E 3 GLN cc_start: 0.6585 (mt0) cc_final: 0.5339 (tp-100) REVERT: E 101 GLN cc_start: 0.6143 (tm-30) cc_final: 0.5707 (tm-30) REVERT: E 133 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: E 164 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8173 (tp) REVERT: F 72 LYS cc_start: 0.7204 (mmtt) cc_final: 0.5877 (mptt) REVERT: F 114 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6595 (mm-30) REVERT: F 127 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8103 (mt-10) REVERT: H 8 ASP cc_start: 0.7934 (t0) cc_final: 0.7613 (t0) REVERT: H 37 LYS cc_start: 0.8339 (ptpt) cc_final: 0.7808 (ptmm) REVERT: H 53 ASP cc_start: 0.8437 (m-30) cc_final: 0.7974 (m-30) REVERT: I 17 ARG cc_start: 0.6618 (tmm-80) cc_final: 0.6211 (tmm-80) REVERT: J 1 MET cc_start: 0.7977 (mtt) cc_final: 0.7341 (mmt) REVERT: J 26 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: J 36 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8778 (mt) REVERT: K 88 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7787 (mttp) REVERT: L 44 ASP cc_start: 0.6503 (t0) cc_final: 0.6263 (t0) outliers start: 58 outliers final: 42 residues processed: 435 average time/residue: 0.1965 time to fit residues: 134.2782 Evaluate side-chains 430 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 381 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 39 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 251 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS A 471 ASN A 650 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101060 restraints weight = 41411.596| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.16 r_work: 0.3135 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30397 Z= 0.258 Angle : 0.628 10.818 41283 Z= 0.326 Chirality : 0.047 0.261 4630 Planarity : 0.005 0.050 5152 Dihedral : 12.207 134.233 4536 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 1.96 % Allowed : 12.88 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3550 helix: 1.04 (0.15), residues: 1217 sheet: -0.18 (0.22), residues: 561 loop : -0.57 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1366 TYR 0.021 0.002 TYR J 44 PHE 0.031 0.002 PHE A 444 TRP 0.013 0.002 TRP B 561 HIS 0.010 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (30365) covalent geometry : angle 0.61775 / 0.33 (41238) hydrogen bonds : bond 0.04789 / 3.34 ( 1244) hydrogen bonds : angle 4.60113 / 3.31 ( 3424) metal coordination : bond 0.00761 / 0.49 ( 32) metal coordination : angle 3.49806 / 2.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 397 time to evaluate : 1.079 Fit side-chains REVERT: A 39 GLU cc_start: 0.7369 (pp20) cc_final: 0.7090 (pm20) REVERT: A 132 LYS cc_start: 0.8215 (mttt) cc_final: 0.7856 (mmtm) REVERT: A 390 GLN cc_start: 0.8343 (tp40) cc_final: 0.7927 (tp40) REVERT: A 695 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8076 (mtmt) REVERT: A 724 GLU cc_start: 0.8108 (tp30) cc_final: 0.7811 (tp30) REVERT: A 829 VAL cc_start: 0.7517 (t) cc_final: 0.7203 (m) REVERT: A 830 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.4569 (pmtt) REVERT: A 895 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8238 (tttp) REVERT: A 978 PRO cc_start: 0.8390 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: A 1063 MET cc_start: 0.8916 (mmm) cc_final: 0.8675 (mmt) REVERT: A 1081 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4445 (tm) REVERT: A 1121 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 1135 ARG cc_start: 0.7794 (tmt170) cc_final: 0.7102 (tmm160) REVERT: A 1159 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6120 (mpt180) REVERT: A 1230 GLU cc_start: 0.5649 (mm-30) cc_final: 0.4717 (tt0) REVERT: A 1411 GLU cc_start: 0.8280 (tp30) cc_final: 0.7904 (mt-10) REVERT: A 1454 MET cc_start: 0.5599 (ttp) cc_final: 0.5184 (tmm) REVERT: B 26 THR cc_start: 0.9016 (p) cc_final: 0.8669 (t) REVERT: B 134 LYS cc_start: 0.6726 (tptp) cc_final: 0.6230 (mttp) REVERT: B 138 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6197 (pt0) REVERT: B 222 ILE cc_start: 0.8236 (mt) cc_final: 0.8017 (pt) REVERT: B 259 TYR cc_start: 0.7407 (m-80) cc_final: 0.7084 (m-80) REVERT: B 270 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7858 (mttp) REVERT: B 313 MET cc_start: 0.8460 (mtp) cc_final: 0.8205 (mtt) REVERT: B 444 MET cc_start: 0.7095 (mmp) cc_final: 0.6445 (pmm) REVERT: B 561 TRP cc_start: 0.6869 (m-10) cc_final: 0.6605 (m100) REVERT: B 641 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: B 666 TYR cc_start: 0.7450 (m-10) cc_final: 0.7218 (m-10) REVERT: B 875 GLU cc_start: 0.8244 (pt0) cc_final: 0.7563 (tt0) REVERT: B 906 SER cc_start: 0.8597 (p) cc_final: 0.8259 (m) REVERT: E 3 GLN cc_start: 0.6723 (mt0) cc_final: 0.5453 (tp-100) REVERT: E 45 LYS cc_start: 0.7574 (tttt) cc_final: 0.7260 (tttm) REVERT: E 133 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: E 164 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8240 (tp) REVERT: F 72 LYS cc_start: 0.7462 (mmtt) cc_final: 0.6158 (mptt) REVERT: F 114 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6663 (mm-30) REVERT: F 127 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8157 (mt-10) REVERT: H 8 ASP cc_start: 0.8079 (t0) cc_final: 0.7660 (t0) REVERT: H 37 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7878 (ptmm) REVERT: H 53 ASP cc_start: 0.8434 (m-30) cc_final: 0.7901 (m-30) REVERT: J 1 MET cc_start: 0.8163 (mtt) cc_final: 0.7403 (mmt) REVERT: K 88 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7794 (mttp) REVERT: L 44 ASP cc_start: 0.6469 (t0) cc_final: 0.6213 (t0) outliers start: 62 outliers final: 45 residues processed: 439 average time/residue: 0.2051 time to fit residues: 141.2170 Evaluate side-chains 430 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 378 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain L residue 39 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 292 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 313 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104515 restraints weight = 41197.670| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.12 r_work: 0.3197 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30397 Z= 0.113 Angle : 0.521 11.024 41283 Z= 0.274 Chirality : 0.042 0.267 4630 Planarity : 0.004 0.051 5152 Dihedral : 12.077 135.000 4536 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.33 % Allowed : 13.58 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3550 helix: 1.37 (0.15), residues: 1211 sheet: -0.07 (0.22), residues: 564 loop : -0.47 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1366 TYR 0.014 0.001 TYR E 46 PHE 0.024 0.001 PHE B 963 TRP 0.013 0.001 TRP A1044 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (30365) covalent geometry : angle 0.51176 / 0.27 (41238) hydrogen bonds : bond 0.03972 / 2.80 ( 1244) hydrogen bonds : angle 4.34669 / 3.14 ( 3424) metal coordination : bond 0.00401 / 0.23 ( 32) metal coordination : angle 3.01491 / 1.97 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 395 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7516 (pp20) cc_final: 0.7243 (pm20) REVERT: A 132 LYS cc_start: 0.8161 (mttt) cc_final: 0.7794 (mmtm) REVERT: A 390 GLN cc_start: 0.8330 (tp40) cc_final: 0.7900 (tp40) REVERT: A 513 SER cc_start: 0.9084 (t) cc_final: 0.8586 (p) REVERT: A 695 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8000 (mtmt) REVERT: A 724 GLU cc_start: 0.8106 (tp30) cc_final: 0.7791 (tp30) REVERT: A 830 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.4423 (pmtt) REVERT: A 895 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8237 (tttp) REVERT: A 965 GLN cc_start: 0.8222 (mt0) cc_final: 0.7826 (mp10) REVERT: A 978 PRO cc_start: 0.8372 (Cg_exo) cc_final: 0.8143 (Cg_endo) REVERT: A 1063 MET cc_start: 0.8825 (mmm) cc_final: 0.8593 (mmt) REVERT: A 1081 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4320 (tm) REVERT: A 1121 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 1135 ARG cc_start: 0.7888 (tmt170) cc_final: 0.7118 (tmm160) REVERT: A 1159 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6126 (mpt180) REVERT: A 1230 GLU cc_start: 0.5411 (mm-30) cc_final: 0.4449 (tt0) REVERT: A 1393 ASN cc_start: 0.8472 (p0) cc_final: 0.8193 (p0) REVERT: A 1454 MET cc_start: 0.5463 (ttp) cc_final: 0.5046 (tmm) REVERT: B 26 THR cc_start: 0.8964 (p) cc_final: 0.8634 (t) REVERT: B 134 LYS cc_start: 0.6702 (tptp) cc_final: 0.6119 (mttt) REVERT: B 138 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6177 (pt0) REVERT: B 259 TYR cc_start: 0.7389 (m-80) cc_final: 0.7114 (m-80) REVERT: B 270 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7923 (mttp) REVERT: B 313 MET cc_start: 0.8393 (mtp) cc_final: 0.8125 (mtt) REVERT: B 346 GLU cc_start: 0.6917 (tp30) cc_final: 0.6086 (mp0) REVERT: B 444 MET cc_start: 0.6981 (mmp) cc_final: 0.6301 (pmm) REVERT: B 531 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6555 (tp40) REVERT: B 597 MET cc_start: 0.8631 (tpt) cc_final: 0.8351 (tpt) REVERT: B 641 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: B 875 GLU cc_start: 0.8077 (pt0) cc_final: 0.7425 (tt0) REVERT: B 906 SER cc_start: 0.8459 (p) cc_final: 0.8152 (m) REVERT: E 3 GLN cc_start: 0.6767 (mt0) cc_final: 0.5443 (tp-100) REVERT: E 164 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8164 (tp) REVERT: F 72 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6034 (mptt) REVERT: F 114 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6579 (mm-30) REVERT: F 127 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8114 (mt-10) REVERT: H 8 ASP cc_start: 0.7996 (t0) cc_final: 0.7624 (t0) REVERT: H 37 LYS cc_start: 0.8344 (ptpt) cc_final: 0.7824 (ptmm) REVERT: H 53 ASP cc_start: 0.8398 (m-30) cc_final: 0.7946 (m-30) REVERT: J 1 MET cc_start: 0.7957 (mtt) cc_final: 0.7369 (mmt) REVERT: K 88 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7791 (mttp) REVERT: L 33 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7476 (mt-10) REVERT: L 44 ASP cc_start: 0.6408 (t0) cc_final: 0.6202 (t0) outliers start: 42 outliers final: 34 residues processed: 427 average time/residue: 0.2048 time to fit residues: 137.3238 Evaluate side-chains 417 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 378 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 830 LYS Chi-restraints excluded: chain A residue 895 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1227 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 250 optimal weight: 0.0010 chunk 255 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103741 restraints weight = 41457.781| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.15 r_work: 0.3174 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30397 Z= 0.145 Angle : 0.532 10.922 41283 Z= 0.278 Chirality : 0.043 0.266 4630 Planarity : 0.004 0.052 5152 Dihedral : 12.053 134.564 4536 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 1.46 % Allowed : 13.83 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3550 helix: 1.39 (0.15), residues: 1210 sheet: -0.02 (0.22), residues: 555 loop : -0.48 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1366 TYR 0.014 0.001 TYR J 44 PHE 0.025 0.001 PHE A 444 TRP 0.013 0.001 TRP B 561 HIS 0.009 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (30365) covalent geometry : angle 0.52384 / 0.28 (41238) hydrogen bonds : bond 0.04020 / 2.83 ( 1244) hydrogen bonds : angle 4.34769 / 3.14 ( 3424) metal coordination : bond 0.00423 / 0.26 ( 32) metal coordination : angle 2.88249 / 1.84 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8109.33 seconds wall clock time: 139 minutes 29.27 seconds (8369.27 seconds total)