Starting phenix.real_space_refine on Thu Oct 29 12:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yd5_72795/10_2026/9yd5_72795.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yd5_72795/10_2026/9yd5_72795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yd5_72795/10_2026/9yd5_72795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yd5_72795/10_2026/9yd5_72795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yd5_72795/10_2026/9yd5_72795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yd5_72795/10_2026/9yd5_72795.map" } resolution = 2.8 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= 0.008 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 76 5.49 5 Mg 1 5.21 5 S 193 5.16 5 C 19622 2.51 5 N 5497 2.21 5 O 6008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31405 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10910 Classifications: {'peptide': 1375} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1306} Chain breaks: 11 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8589 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1022} Chain breaks: 12 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2015 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 15, 'TRANS': 235} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1672 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain breaks: 1 Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1181 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "I" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain breaks: 3 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 354 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain breaks: 2 Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 510 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "P" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 320 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 108.351 80.376 78.569 1.00166.91 S ATOM 486 SG CYS A 74 107.831 77.515 76.944 1.00142.90 S ATOM 533 SG CYS A 81 104.707 79.228 77.087 1.00146.16 S ATOM 768 SG CYS A 111 97.018 68.704 123.402 1.00208.68 S ATOM 1029 SG CYS A 154 96.280 66.891 125.095 1.00218.10 S ATOM 1062 SG CYS A 184 98.967 66.816 125.796 1.00218.55 S ATOM 19076 SG CYS B1119 107.727 64.506 85.936 1.00161.29 S ATOM 19098 SG CYS B1122 105.957 66.142 88.648 1.00171.85 S ATOM 19213 SG CYS B1137 108.016 67.539 86.913 1.00177.90 S ATOM 19234 SG CYS B1140 108.071 66.503 89.790 1.00187.19 S ATOM 20193 SG CYS C 88 72.151 90.901 19.812 1.00182.71 S ATOM 20241 SG CYS C 94 72.278 93.858 19.684 1.00182.41 S ATOM 27767 SG CYS I 86 12.093 98.328 107.619 1.00177.70 S ATOM 27791 SG CYS I 89 11.136 101.310 106.374 1.00176.33 S ATOM 27957 SG CYS I 114 13.452 101.104 104.547 1.00173.70 S ATOM 27992 SG CYS I 119 13.141 101.272 107.789 1.00171.03 S ATOM 27332 SG CYS I 17 43.044 104.024 138.298 1.00202.90 S ATOM 27456 SG CYS I 39 44.917 102.106 139.067 1.00212.90 S ATOM 27481 SG CYS I 42 45.496 103.525 141.458 1.00203.11 S ATOM 28102 SG CYS J 7 46.207 93.755 41.089 1.00114.97 S ATOM 28126 SG CYS J 10 45.013 93.371 38.536 1.00127.60 S ATOM 28390 SG CYS J 44 43.331 91.770 41.490 1.00125.20 S ATOM 29516 SG CYS L 19 74.616 124.885 55.297 1.00178.69 S ATOM 29526 SG CYS L 22 73.941 127.205 54.234 1.00182.49 S ATOM 29643 SG CYS L 36 77.294 124.785 55.489 1.00180.69 S ATOM 29660 SG CYS L 39 73.594 127.082 56.818 1.00197.17 S Time building chain proxies: 6.36, per 1000 atoms: 0.20 Number of scatterers: 31405 At special positions: 0 Unit cell: (171.798, 147.96, 157.002, 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 193 16.00 P 76 15.00 Mg 1 11.99 O 6008 8.00 N 5497 7.00 C 19622 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: 3.21 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 18 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7036 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 46 sheets defined 40.1% alpha, 15.8% beta 32 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.771A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.600A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.644A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.840A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.759A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.693A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 853 removed outlier: 3.534A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 869 Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.670A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.574A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.509A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.039A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.904A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.801A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 4.300A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 3.678A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.673A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1349 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.836A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.036A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.778A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.519A pdb=" N GLY B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.800A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 358 through 378 removed outlier: 3.583A pdb=" N LEU B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.989A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.874A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.742A pdb=" N ILE B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.946A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 606 through 610 removed outlier: 3.594A pdb=" N ARG B 610 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.739A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.726A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.520A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 768 removed outlier: 3.639A pdb=" N ARG B 768 " --> pdb=" O GLU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.205A pdb=" N LYS B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.623A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.773A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1018 removed outlier: 3.661A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.606A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.941A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 265 removed outlier: 3.576A pdb=" N HIS C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.554A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.828A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.960A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.825A pdb=" N LEU E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 136' Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.053A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.766A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 134' Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.613A pdb=" N ILE I 68 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.627A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.376A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.564A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 9.761A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.605A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.723A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 6.033A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.204A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.711A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 Processing sheet with id=AB2, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.946A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 4.182A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1170 through 1177 Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1471 through 1475 removed outlier: 3.552A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 93 removed outlier: 4.381A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.487A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC8, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.508A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 602 through 603 Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.747A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 5.797A pdb=" N VAL B 794 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.980A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.608A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 44 through 55 removed outlier: 6.227A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 removed outlier: 7.010A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.719A pdb=" N VAL G 58 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.493A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.877A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.876A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AE7, first strand: chain 'H' and resid 42 through 44 removed outlier: 3.589A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP H 14 " --> pdb=" O HIS H 29 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 26 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 21 through 23 1260 hydrogen bonds defined for protein. 3480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 10.78 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10148 1.34 - 1.46: 7267 1.46 - 1.59: 14269 1.59 - 1.71: 146 1.71 - 1.83: 304 Bond restraints: 32134 Sorted by residual: bond pdb=" C1' DT N 7 " pdb=" N1 DT N 7 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" C1' DG N 14 " pdb=" N9 DG N 14 " ideal model delta sigma weight residual 1.468 1.389 0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" C1' DC T 35 " pdb=" N1 DC T 35 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.13e+01 bond pdb=" C1' DC N 9 " pdb=" N1 DC N 9 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.10e+01 bond pdb=" C1' DC N 12 " pdb=" N1 DC N 12 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.96e+01 ... (remaining 32129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 42610 1.56 - 3.11: 830 3.11 - 4.67: 222 4.67 - 6.22: 31 6.22 - 7.78: 18 Bond angle restraints: 43711 Sorted by residual: angle pdb=" CA ASP A 497 " pdb=" CB ASP A 497 " pdb=" CG ASP A 497 " ideal model delta sigma weight residual 112.60 117.28 -4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" N ALA B 496 " pdb=" CA ALA B 496 " pdb=" C ALA B 496 " ideal model delta sigma weight residual 113.17 107.35 5.82 1.26e+00 6.30e-01 2.14e+01 angle pdb=" CA THR A1100 " pdb=" CB THR A1100 " pdb=" OG1 THR A1100 " ideal model delta sigma weight residual 109.60 102.67 6.93 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C CYS I 20 " pdb=" CA CYS I 20 " pdb=" CB CYS I 20 " ideal model delta sigma weight residual 110.63 102.90 7.73 1.85e+00 2.92e-01 1.75e+01 angle pdb=" N3 DT T 16 " pdb=" C4 DT T 16 " pdb=" O4 DT T 16 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 43706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 18384 35.32 - 70.64: 1064 70.64 - 105.97: 62 105.97 - 141.29: 1 141.29 - 176.61: 3 Dihedral angle restraints: 19514 sinusoidal: 8662 harmonic: 10852 Sorted by residual: dihedral pdb=" O4' U P 35 " pdb=" C1' U P 35 " pdb=" N1 U P 35 " pdb=" C2 U P 35 " ideal model delta sinusoidal sigma weight residual -128.00 -63.93 -64.07 1 1.70e+01 3.46e-03 1.87e+01 dihedral pdb=" CA SER B 228 " pdb=" C SER B 228 " pdb=" N SER B 229 " pdb=" CA SER B 229 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS A1350 " pdb=" C LYS A1350 " pdb=" N ASP A1351 " pdb=" CA ASP A1351 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 19511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 4839 0.127 - 0.253: 72 0.253 - 0.380: 0 0.380 - 0.506: 4 0.506 - 0.633: 8 Chirality restraints: 4923 Sorted by residual: chirality pdb=" P DC N 12 " pdb=" OP1 DC N 12 " pdb=" OP2 DC N 12 " pdb=" O5' DC N 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DG N 26 " pdb=" OP1 DG N 26 " pdb=" OP2 DG N 26 " pdb=" O5' DG N 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" P DT N 11 " pdb=" OP1 DT N 11 " pdb=" OP2 DT N 11 " pdb=" O5' DT N 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.12e+00 ... (remaining 4920 not shown) Planarity restraints: 5368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1133 " 0.065 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A1134 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A1134 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1134 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1133 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.39e+00 pdb=" C LYS A1133 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS A1133 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A1134 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 16 " 0.179 9.50e-02 1.11e+02 8.04e-02 4.38e+00 pdb=" NE ARG A 16 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 16 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 16 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 16 " 0.003 2.00e-02 2.50e+03 ... (remaining 5365 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 34 2.43 - 3.05: 21152 3.05 - 3.67: 47468 3.67 - 4.28: 72630 4.28 - 4.90: 122581 Nonbonded interactions: 263865 Sorted by model distance: nonbonded pdb=" CB CYS I 20 " pdb="ZN ZN I 202 " model vdw 1.814 2.630 nonbonded pdb=" N CYS J 10 " pdb="ZN ZN J 101 " model vdw 1.887 2.310 nonbonded pdb=" SG CYS L 22 " pdb=" CB CYS L 39 " model vdw 2.009 3.040 nonbonded pdb=" OD2 ASP A 495 " pdb="MG MG A2003 " model vdw 2.031 2.170 nonbonded pdb=" N CYS I 20 " pdb="ZN ZN I 202 " model vdw 2.041 2.310 ... (remaining 263860 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: 6.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 43.020 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.010 0.990 32160 Z= 0.407 Angle : 0.944 68.038 43729 Z= 0.377 Chirality : 0.052 0.633 4923 Planarity : 0.004 0.099 5368 Dihedral : 19.602 176.611 12478 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.58 % Allowed : 27.09 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 (0.15), residues: 3646 helix: 1.62 (0.15), residues: 1320 sheet: -1.26 (0.23), residues: 527 loop : -0.87 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 16 TYR 0.015 0.001 TYR E 26 PHE 0.019 0.001 PHE A 113 TRP 0.012 0.001 TRP B 27 HIS 0.008 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.26 (32134) covalent geometry : angle 0.58568 / 0.35 (43711) hydrogen bonds : bond 0.13233 / 9.08 ( 1328) hydrogen bonds : angle 6.32660 / 4.57 ( 3644) metal coordination : bond 0.32557 / 20.53 ( 26) metal coordination : angle 36.51344 / 24.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 401 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.9124 (mmt90) cc_final: 0.8896 (mmt-90) REVERT: A 138 LYS cc_start: 0.7672 (tttt) cc_final: 0.6824 (tptt) REVERT: A 238 MET cc_start: 0.8530 (mtm) cc_final: 0.8235 (mtt) REVERT: A 274 ASP cc_start: 0.8804 (t70) cc_final: 0.8348 (t0) REVERT: A 329 MET cc_start: 0.8588 (mmm) cc_final: 0.8301 (mmm) REVERT: A 404 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: A 425 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6604 (m-30) REVERT: A 524 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8534 (mtp) REVERT: A 735 GLN cc_start: 0.8367 (mm110) cc_final: 0.7627 (mt0) REVERT: A 740 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: A 853 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5646 (ptpt) REVERT: A 986 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8498 (mtt) REVERT: A 1255 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7454 (tt) REVERT: A 1285 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7812 (tm) REVERT: A 1309 MET cc_start: 0.8742 (tpp) cc_final: 0.8038 (tmt) REVERT: A 1364 GLU cc_start: 0.8238 (tt0) cc_final: 0.7859 (tt0) REVERT: A 1379 GLU cc_start: 0.8653 (tt0) cc_final: 0.8399 (tt0) REVERT: B 377 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 438 ARG cc_start: 0.6934 (pmt170) cc_final: 0.6604 (pmt170) REVERT: B 508 MET cc_start: 0.9343 (mmt) cc_final: 0.8797 (mmt) REVERT: B 609 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8102 (tt0) REVERT: B 681 ASP cc_start: 0.8160 (m-30) cc_final: 0.7819 (m-30) REVERT: B 892 CYS cc_start: 0.8658 (m) cc_final: 0.8186 (p) REVERT: B 900 GLU cc_start: 0.8498 (mp0) cc_final: 0.7664 (mp0) REVERT: B 919 CYS cc_start: 0.9001 (t) cc_final: 0.8732 (p) REVERT: C 41 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: D 62 MET cc_start: 0.7472 (tpp) cc_final: 0.7073 (tmm) REVERT: D 109 GLU cc_start: 0.6601 (tt0) cc_final: 0.5845 (mp0) REVERT: E 18 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8891 (tpp) REVERT: E 44 PHE cc_start: 0.8666 (m-80) cc_final: 0.8264 (m-80) REVERT: E 88 LYS cc_start: 0.9182 (tptm) cc_final: 0.8663 (mtmt) REVERT: E 91 CYS cc_start: 0.8918 (t) cc_final: 0.8655 (m) REVERT: E 121 MET cc_start: 0.8148 (pmm) cc_final: 0.7920 (pmm) REVERT: E 159 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8542 (tp) REVERT: F 61 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8457 (mt-10) REVERT: G 11 ILE cc_start: 0.7382 (tp) cc_final: 0.7119 (pp) REVERT: G 131 MET cc_start: 0.1772 (ptp) cc_final: 0.0604 (mmm) REVERT: H 37 MET cc_start: 0.8691 (mmm) cc_final: 0.8464 (mtp) REVERT: H 57 ARG cc_start: 0.8298 (ttt-90) cc_final: 0.7661 (ttm-80) REVERT: H 66 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.4070 (mp0) REVERT: H 81 ARG cc_start: 0.8521 (mmm160) cc_final: 0.8018 (mmp80) REVERT: H 103 GLU cc_start: 0.8143 (mp0) cc_final: 0.7894 (pm20) REVERT: I 18 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7929 (mm-40) REVERT: I 64 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5901 (mp0) REVERT: I 66 THR cc_start: 0.9208 (p) cc_final: 0.8811 (p) REVERT: I 67 GLN cc_start: 0.9098 (pt0) cc_final: 0.8532 (pm20) REVERT: I 69 ILE cc_start: 0.8903 (mm) cc_final: 0.8620 (mm) REVERT: I 109 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8301 (ttm-80) REVERT: I 122 ARG cc_start: 0.8739 (ptp90) cc_final: 0.8479 (ptp90) REVERT: J 28 GLU cc_start: 0.9101 (mp0) cc_final: 0.8775 (mp0) REVERT: K 16 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8343 (mt-10) REVERT: L 26 ASN cc_start: 0.8554 (t0) cc_final: 0.8128 (m-40) REVERT: L 31 ARG cc_start: 0.8741 (tmm160) cc_final: 0.8391 (tmm-80) REVERT: L 34 ILE cc_start: 0.8603 (mm) cc_final: 0.8275 (mm) REVERT: L 42 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7883 (mmt90) REVERT: L 47 LYS cc_start: 0.8967 (tttm) cc_final: 0.8662 (tttt) outliers start: 52 outliers final: 25 residues processed: 437 average time/residue: 0.6896 time to fit residues: 355.1661 Evaluate side-chains 410 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 372 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 HIS A 507 GLN A 529 GLN A1163 HIS A1172 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS C 5 ASN D 43 HIS E 116 GLN G 21 ASN H 76 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS K 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077205 restraints weight = 54604.494| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.64 r_work: 0.2926 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32160 Z= 0.218 Angle : 0.707 30.402 43729 Z= 0.323 Chirality : 0.045 0.294 4923 Planarity : 0.004 0.073 5368 Dihedral : 15.078 177.858 5050 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.01 % Allowed : 24.03 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.07 (0.14), residues: 3646 helix: 1.58 (0.15), residues: 1335 sheet: -1.04 (0.23), residues: 504 loop : -0.78 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 222 TYR 0.016 0.001 TYR H 90 PHE 0.019 0.002 PHE G 77 TRP 0.013 0.001 TRP B 27 HIS 0.008 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (32134) covalent geometry : angle 0.60722 / 0.32 (43711) hydrogen bonds : bond 0.04754 / 3.14 ( 1328) hydrogen bonds : angle 5.00385 / 3.60 ( 3644) metal coordination : bond 0.01625 / 1.11 ( 26) metal coordination : angle 17.89800 / 11.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 403 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7381 (mm) REVERT: A 138 LYS cc_start: 0.7434 (tttt) cc_final: 0.6618 (tptt) REVERT: A 274 ASP cc_start: 0.8246 (t70) cc_final: 0.7640 (t0) REVERT: A 327 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8026 (mtt-85) REVERT: A 329 MET cc_start: 0.8545 (mmm) cc_final: 0.8253 (mmm) REVERT: A 425 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6179 (m-30) REVERT: A 524 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: A 735 GLN cc_start: 0.8172 (mm110) cc_final: 0.7372 (mt0) REVERT: A 740 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: A 853 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5642 (ptpt) REVERT: A 986 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8201 (mtt) REVERT: A 1285 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7794 (tm) REVERT: A 1309 MET cc_start: 0.8600 (tpp) cc_final: 0.7929 (tmt) REVERT: A 1351 ASP cc_start: 0.8656 (m-30) cc_final: 0.8273 (t0) REVERT: A 1361 ASP cc_start: 0.8571 (t0) cc_final: 0.8282 (t0) REVERT: A 1379 GLU cc_start: 0.8346 (tt0) cc_final: 0.8104 (tt0) REVERT: A 1380 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7535 (mtp180) REVERT: B 337 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7667 (tppt) REVERT: B 377 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 497 LYS cc_start: 0.8054 (pttp) cc_final: 0.7826 (pptt) REVERT: B 609 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8084 (tt0) REVERT: B 612 ILE cc_start: 0.8960 (mt) cc_final: 0.8726 (mp) REVERT: B 899 SER cc_start: 0.8446 (m) cc_final: 0.8164 (p) REVERT: B 900 GLU cc_start: 0.8403 (mp0) cc_final: 0.7495 (mp0) REVERT: B 919 CYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8479 (p) REVERT: D 62 MET cc_start: 0.7484 (tpp) cc_final: 0.7140 (tmm) REVERT: D 109 GLU cc_start: 0.6519 (tt0) cc_final: 0.5832 (mp0) REVERT: E 18 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (tpp) REVERT: E 44 PHE cc_start: 0.8634 (m-80) cc_final: 0.8225 (m-80) REVERT: E 88 LYS cc_start: 0.9121 (tptm) cc_final: 0.8611 (mtmt) REVERT: E 91 CYS cc_start: 0.8931 (t) cc_final: 0.8657 (m) REVERT: E 177 ASP cc_start: 0.8414 (t0) cc_final: 0.8150 (t0) REVERT: F 61 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8189 (mt-10) REVERT: F 109 TYR cc_start: 0.8801 (m-80) cc_final: 0.8560 (m-80) REVERT: G 131 MET cc_start: 0.1759 (ptp) cc_final: 0.0880 (mmm) REVERT: H 7 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 35 PHE cc_start: 0.7787 (m-80) cc_final: 0.7531 (m-80) REVERT: H 37 MET cc_start: 0.8414 (mmm) cc_final: 0.8167 (mtp) REVERT: H 57 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.7162 (ttm-80) REVERT: H 65 TYR cc_start: 0.8457 (m-10) cc_final: 0.8190 (m-10) REVERT: H 66 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.3630 (mp0) REVERT: H 76 ASN cc_start: 0.7953 (t0) cc_final: 0.7477 (p0) REVERT: H 81 ARG cc_start: 0.8509 (mmm160) cc_final: 0.7987 (mmp80) REVERT: H 103 GLU cc_start: 0.8106 (mp0) cc_final: 0.7821 (pm20) REVERT: I 18 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7923 (mm-40) REVERT: I 45 GLN cc_start: 0.8767 (mp10) cc_final: 0.8483 (mp10) REVERT: I 64 GLU cc_start: 0.5447 (mm-30) cc_final: 0.5121 (mp0) REVERT: I 66 THR cc_start: 0.9041 (p) cc_final: 0.8668 (p) REVERT: I 67 GLN cc_start: 0.8769 (pt0) cc_final: 0.8276 (pm20) REVERT: I 69 ILE cc_start: 0.8496 (mm) cc_final: 0.8234 (mm) REVERT: I 71 ASP cc_start: 0.8861 (m-30) cc_final: 0.8370 (m-30) REVERT: I 109 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7899 (ttm-80) REVERT: I 122 ARG cc_start: 0.8545 (ptp90) cc_final: 0.8267 (ptp90) REVERT: K 16 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8234 (mt-10) REVERT: K 55 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: L 26 ASN cc_start: 0.8413 (t0) cc_final: 0.7911 (m-40) REVERT: L 27 GLU cc_start: 0.8281 (tp30) cc_final: 0.8009 (tp30) REVERT: L 31 ARG cc_start: 0.8604 (tmm160) cc_final: 0.8253 (tmm-80) REVERT: L 34 ILE cc_start: 0.8353 (mm) cc_final: 0.7975 (mm) REVERT: L 42 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7412 (mmt90) REVERT: L 47 LYS cc_start: 0.8682 (tttm) cc_final: 0.8368 (tttt) REVERT: L 56 ASP cc_start: 0.8312 (p0) cc_final: 0.8083 (p0) outliers start: 165 outliers final: 68 residues processed: 527 average time/residue: 0.6454 time to fit residues: 406.3545 Evaluate side-chains 466 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 382 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1074 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [156, 141, 315, 79, 97, 374, 5, 60, 303, 12, 354] chunk 156 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 374 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 354 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1093 GLN A1163 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS G 21 ASN G 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077542 restraints weight = 54046.125| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.75 r_work: 0.2896 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32160 Z= 0.180 Angle : 0.606 19.569 43729 Z= 0.300 Chirality : 0.044 0.281 4923 Planarity : 0.004 0.067 5368 Dihedral : 15.109 178.576 5034 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.79 % Allowed : 24.70 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.11 (0.14), residues: 3646 helix: 1.57 (0.15), residues: 1342 sheet: -0.97 (0.23), residues: 500 loop : -0.74 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1141 TYR 0.015 0.001 TYR E 90 PHE 0.019 0.001 PHE C 93 TRP 0.017 0.001 TRP B 236 HIS 0.008 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (32134) covalent geometry : angle 0.56988 / 0.30 (43711) hydrogen bonds : bond 0.04232 / 2.82 ( 1328) hydrogen bonds : angle 4.75699 / 3.41 ( 3644) metal coordination : bond 0.01072 / 0.76 ( 26) metal coordination : angle 10.23488 / 6.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 400 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7431 (tttt) cc_final: 0.6612 (tptt) REVERT: A 274 ASP cc_start: 0.8126 (t70) cc_final: 0.7435 (t0) REVERT: A 329 MET cc_start: 0.8538 (mmm) cc_final: 0.8255 (mmm) REVERT: A 425 ASP cc_start: 0.6390 (OUTLIER) cc_final: 0.6117 (m-30) REVERT: A 734 ARG cc_start: 0.6352 (mpt180) cc_final: 0.6070 (mpt180) REVERT: A 735 GLN cc_start: 0.8185 (mm110) cc_final: 0.7428 (mt0) REVERT: A 853 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.5733 (ptpt) REVERT: A 986 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8227 (mtt) REVERT: A 1253 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5808 (pp20) REVERT: A 1351 ASP cc_start: 0.8648 (m-30) cc_final: 0.8314 (t0) REVERT: A 1361 ASP cc_start: 0.8606 (t0) cc_final: 0.8254 (t0) REVERT: A 1379 GLU cc_start: 0.8388 (tt0) cc_final: 0.8149 (tt0) REVERT: A 1441 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 337 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7667 (tppt) REVERT: B 344 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: B 377 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 380 ARG cc_start: 0.8829 (ttt180) cc_final: 0.8423 (ttt180) REVERT: B 497 LYS cc_start: 0.8058 (pttp) cc_final: 0.7804 (pptt) REVERT: B 645 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 681 ASP cc_start: 0.8072 (m-30) cc_final: 0.7698 (m-30) REVERT: B 899 SER cc_start: 0.8553 (m) cc_final: 0.8274 (p) REVERT: B 900 GLU cc_start: 0.8483 (mp0) cc_final: 0.7553 (mp0) REVERT: B 919 CYS cc_start: 0.9004 (t) cc_final: 0.8457 (p) REVERT: B 1088 GLU cc_start: 0.7582 (tt0) cc_final: 0.6856 (tm-30) REVERT: C 91 GLU cc_start: 0.8761 (tp30) cc_final: 0.8527 (pp20) REVERT: C 201 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8773 (pm20) REVERT: D 62 MET cc_start: 0.7455 (tpp) cc_final: 0.7103 (tmm) REVERT: D 109 GLU cc_start: 0.6484 (tt0) cc_final: 0.5827 (mp0) REVERT: E 18 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8415 (mpt) REVERT: E 23 ASP cc_start: 0.8829 (m-30) cc_final: 0.8477 (m-30) REVERT: E 43 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: E 44 PHE cc_start: 0.8621 (m-80) cc_final: 0.7967 (m-80) REVERT: E 177 ASP cc_start: 0.8445 (t0) cc_final: 0.8175 (t0) REVERT: F 61 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8273 (mt-10) REVERT: G 131 MET cc_start: 0.1627 (ptp) cc_final: 0.0725 (mmm) REVERT: H 7 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8349 (tm-30) REVERT: H 35 PHE cc_start: 0.7817 (m-80) cc_final: 0.7459 (m-80) REVERT: H 57 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7211 (ttm-80) REVERT: H 65 TYR cc_start: 0.8467 (m-10) cc_final: 0.8206 (m-10) REVERT: H 66 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.3584 (mp0) REVERT: H 76 ASN cc_start: 0.8004 (t0) cc_final: 0.7548 (p0) REVERT: H 81 ARG cc_start: 0.8509 (mmm160) cc_final: 0.7999 (mmp80) REVERT: H 103 GLU cc_start: 0.8070 (mp0) cc_final: 0.7786 (pm20) REVERT: I 15 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7560 (mpt-90) REVERT: I 18 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8078 (mm-40) REVERT: I 45 GLN cc_start: 0.8847 (mp10) cc_final: 0.8517 (mp10) REVERT: I 64 GLU cc_start: 0.5472 (mm-30) cc_final: 0.5204 (mp0) REVERT: I 66 THR cc_start: 0.9077 (p) cc_final: 0.8658 (p) REVERT: I 67 GLN cc_start: 0.8747 (pt0) cc_final: 0.8264 (pm20) REVERT: I 69 ILE cc_start: 0.8539 (mm) cc_final: 0.8259 (mm) REVERT: I 71 ASP cc_start: 0.8876 (m-30) cc_final: 0.8391 (m-30) REVERT: I 109 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8011 (ttm-80) REVERT: K 16 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: L 26 ASN cc_start: 0.8472 (t0) cc_final: 0.7988 (t0) REVERT: L 27 GLU cc_start: 0.8400 (tp30) cc_final: 0.8113 (tp30) REVERT: L 31 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8283 (tmm-80) REVERT: L 34 ILE cc_start: 0.8409 (mm) cc_final: 0.7870 (mm) REVERT: L 42 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7033 (mmt-90) REVERT: L 47 LYS cc_start: 0.8721 (tttm) cc_final: 0.8405 (tttt) REVERT: L 56 ASP cc_start: 0.8407 (p0) cc_final: 0.8169 (p0) outliers start: 158 outliers final: 78 residues processed: 527 average time/residue: 0.6515 time to fit residues: 406.5949 Evaluate side-chains 473 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 379 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [114, 214, 72, 58, 209, 226, 78, 143, 310, 349, 186] chunk 114 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 310 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1163 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 725 GLN C 5 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS H 130 ASN I 22 ASN I 87 GLN I 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079120 restraints weight = 53578.922| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.74 r_work: 0.2931 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32160 Z= 0.126 Angle : 0.578 14.966 43729 Z= 0.290 Chirality : 0.043 0.283 4923 Planarity : 0.004 0.066 5368 Dihedral : 15.075 177.433 5025 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.55 % Allowed : 25.55 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.24 (0.14), residues: 3646 helix: 1.63 (0.15), residues: 1349 sheet: -0.85 (0.23), residues: 498 loop : -0.65 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1141 TYR 0.020 0.001 TYR H 90 PHE 0.022 0.001 PHE A 113 TRP 0.021 0.001 TRP B 236 HIS 0.007 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (32134) covalent geometry : angle 0.55850 / 0.29 (43711) hydrogen bonds : bond 0.03785 / 2.52 ( 1328) hydrogen bonds : angle 4.55784 / 3.27 ( 3644) metal coordination : bond 0.00771 / 0.55 ( 26) metal coordination : angle 7.38162 / 4.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 403 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8551 (mm-30) REVERT: A 138 LYS cc_start: 0.7349 (tttt) cc_final: 0.6562 (tptt) REVERT: A 274 ASP cc_start: 0.8078 (t70) cc_final: 0.7358 (t0) REVERT: A 321 GLU cc_start: 0.8650 (pp20) cc_final: 0.8369 (pp20) REVERT: A 327 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8087 (mtt-85) REVERT: A 329 MET cc_start: 0.8549 (mmm) cc_final: 0.8261 (mmm) REVERT: A 425 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6126 (m-30) REVERT: A 735 GLN cc_start: 0.8166 (mm110) cc_final: 0.7408 (mt0) REVERT: A 853 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5723 (ptpt) REVERT: A 927 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: A 986 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8237 (mtt) REVERT: A 1139 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 1160 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8426 (ttm-80) REVERT: A 1253 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5834 (pp20) REVERT: A 1309 MET cc_start: 0.8608 (tpp) cc_final: 0.8394 (tpp) REVERT: A 1351 ASP cc_start: 0.8606 (m-30) cc_final: 0.8236 (t0) REVERT: A 1361 ASP cc_start: 0.8613 (t0) cc_final: 0.8095 (t0) REVERT: A 1364 GLU cc_start: 0.8175 (tt0) cc_final: 0.7746 (tt0) REVERT: A 1379 GLU cc_start: 0.8427 (tt0) cc_final: 0.8193 (tt0) REVERT: A 1380 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7549 (mtp180) REVERT: A 1472 ASP cc_start: 0.8400 (m-30) cc_final: 0.8161 (m-30) REVERT: B 53 MET cc_start: 0.7923 (mpp) cc_final: 0.7106 (mpp) REVERT: B 337 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7655 (tppt) REVERT: B 344 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: B 377 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 497 LYS cc_start: 0.8074 (pttp) cc_final: 0.7812 (pptt) REVERT: B 609 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8161 (tt0) REVERT: B 645 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: B 681 ASP cc_start: 0.8048 (m-30) cc_final: 0.7687 (m-30) REVERT: B 709 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8795 (m) REVERT: B 899 SER cc_start: 0.8625 (m) cc_final: 0.8362 (p) REVERT: B 900 GLU cc_start: 0.8517 (mp0) cc_final: 0.7564 (mp0) REVERT: B 1088 GLU cc_start: 0.7533 (tt0) cc_final: 0.6838 (tm-30) REVERT: B 1136 GLU cc_start: 0.7543 (tp30) cc_final: 0.7051 (tm-30) REVERT: C 91 GLU cc_start: 0.8769 (tp30) cc_final: 0.8542 (pt0) REVERT: C 96 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7944 (pp20) REVERT: C 201 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: D 62 MET cc_start: 0.7466 (tpp) cc_final: 0.7121 (tmm) REVERT: D 109 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: E 18 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8430 (mpt) REVERT: E 23 ASP cc_start: 0.8796 (m-30) cc_final: 0.8434 (m-30) REVERT: E 43 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: E 44 PHE cc_start: 0.8632 (m-80) cc_final: 0.7931 (m-80) REVERT: E 95 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8611 (mm110) REVERT: E 125 TYR cc_start: 0.7371 (m-80) cc_final: 0.6854 (m-10) REVERT: E 177 ASP cc_start: 0.8433 (t0) cc_final: 0.8159 (t0) REVERT: F 61 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8284 (mt-10) REVERT: G 131 MET cc_start: 0.1578 (ptp) cc_final: 0.0725 (mmm) REVERT: H 7 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8406 (tm-30) REVERT: H 57 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7202 (ttm-80) REVERT: H 65 TYR cc_start: 0.8438 (m-10) cc_final: 0.8191 (m-10) REVERT: H 66 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.3599 (mp0) REVERT: H 76 ASN cc_start: 0.8010 (t0) cc_final: 0.7563 (p0) REVERT: H 81 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8022 (mmp80) REVERT: H 103 GLU cc_start: 0.8029 (mp0) cc_final: 0.7737 (pm20) REVERT: I 15 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7667 (mpt-90) REVERT: I 18 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8144 (mm-40) REVERT: I 66 THR cc_start: 0.9112 (p) cc_final: 0.8676 (p) REVERT: I 67 GLN cc_start: 0.8755 (pt0) cc_final: 0.8281 (pm20) REVERT: I 69 ILE cc_start: 0.8490 (mm) cc_final: 0.8213 (mm) REVERT: I 109 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8020 (ttm-80) REVERT: K 16 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: L 26 ASN cc_start: 0.8473 (t0) cc_final: 0.7953 (m-40) REVERT: L 27 GLU cc_start: 0.8431 (tp30) cc_final: 0.8201 (tp30) REVERT: L 31 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8249 (tmm-80) REVERT: L 34 ILE cc_start: 0.8441 (mm) cc_final: 0.7976 (mm) REVERT: L 42 ARG cc_start: 0.7728 (mmt-90) cc_final: 0.7175 (mmt-90) REVERT: L 47 LYS cc_start: 0.8732 (tttm) cc_final: 0.8402 (tttt) REVERT: L 56 ASP cc_start: 0.8503 (p0) cc_final: 0.8248 (p0) outliers start: 150 outliers final: 74 residues processed: 521 average time/residue: 0.6487 time to fit residues: 402.3430 Evaluate side-chains 479 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 381 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [117, 241, 158, 101, 368, 325, 168, 122, 277, 82, 226] chunk 117 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 HIS A1163 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B1073 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS G 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076058 restraints weight = 54253.513| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.74 r_work: 0.2878 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 32160 Z= 0.296 Angle : 0.644 13.817 43729 Z= 0.324 Chirality : 0.046 0.288 4923 Planarity : 0.004 0.063 5368 Dihedral : 15.132 178.807 5023 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.25 % Allowed : 25.70 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.05 (0.14), residues: 3646 helix: 1.49 (0.15), residues: 1340 sheet: -0.93 (0.24), residues: 473 loop : -0.77 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 16 TYR 0.014 0.002 TYR J 43 PHE 0.022 0.002 PHE C 93 TRP 0.020 0.001 TRP B 236 HIS 0.010 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.30 (32134) covalent geometry : angle 0.62494 / 0.32 (43711) hydrogen bonds : bond 0.04318 / 2.89 ( 1328) hydrogen bonds : angle 4.67837 / 3.36 ( 3644) metal coordination : bond 0.01306 / 0.94 ( 26) metal coordination : angle 7.79019 / 4.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 379 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7449 (tttt) cc_final: 0.6661 (tptt) REVERT: A 274 ASP cc_start: 0.8131 (t70) cc_final: 0.7423 (t0) REVERT: A 321 GLU cc_start: 0.8681 (pp20) cc_final: 0.8402 (pp20) REVERT: A 329 MET cc_start: 0.8505 (mmm) cc_final: 0.8251 (mmm) REVERT: A 425 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6140 (m-30) REVERT: A 735 GLN cc_start: 0.8201 (mm110) cc_final: 0.7403 (mt0) REVERT: A 740 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: A 853 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.5683 (ptpt) REVERT: A 927 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: A 986 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8224 (mtt) REVERT: A 1094 SER cc_start: 0.9018 (m) cc_final: 0.8646 (p) REVERT: A 1139 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 1160 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8401 (ttm-80) REVERT: A 1253 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5934 (pp20) REVERT: A 1351 ASP cc_start: 0.8649 (m-30) cc_final: 0.8262 (t0) REVERT: A 1361 ASP cc_start: 0.8700 (t0) cc_final: 0.8196 (t0) REVERT: A 1364 GLU cc_start: 0.8212 (tt0) cc_final: 0.7717 (tt0) REVERT: A 1379 GLU cc_start: 0.8412 (tt0) cc_final: 0.8157 (tt0) REVERT: A 1380 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7602 (mtp180) REVERT: A 1441 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 1472 ASP cc_start: 0.8402 (m-30) cc_final: 0.8197 (m-30) REVERT: B 314 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: B 337 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7554 (tppt) REVERT: B 344 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: B 377 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 497 LYS cc_start: 0.8121 (pttp) cc_final: 0.7823 (pptt) REVERT: B 555 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7117 (pp20) REVERT: B 609 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8149 (tt0) REVERT: B 645 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 899 SER cc_start: 0.8530 (m) cc_final: 0.8310 (p) REVERT: B 900 GLU cc_start: 0.8527 (mp0) cc_final: 0.7534 (mp0) REVERT: B 1088 GLU cc_start: 0.7656 (tt0) cc_final: 0.6901 (tm-30) REVERT: B 1136 GLU cc_start: 0.7769 (tp30) cc_final: 0.7518 (tm-30) REVERT: B 1143 LYS cc_start: 0.8007 (mptt) cc_final: 0.7624 (tppt) REVERT: C 96 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: C 201 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8765 (pm20) REVERT: D 32 LEU cc_start: 0.2787 (OUTLIER) cc_final: 0.2586 (mt) REVERT: D 62 MET cc_start: 0.7404 (tpp) cc_final: 0.7037 (tmm) REVERT: D 119 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5565 (tm-30) REVERT: E 18 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8397 (mpt) REVERT: E 23 ASP cc_start: 0.8806 (m-30) cc_final: 0.8482 (m-30) REVERT: E 43 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: E 44 PHE cc_start: 0.8618 (m-80) cc_final: 0.7932 (m-80) REVERT: E 91 CYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8790 (m) REVERT: E 107 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: E 125 TYR cc_start: 0.7526 (m-80) cc_final: 0.7297 (m-10) REVERT: E 158 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: E 177 ASP cc_start: 0.8460 (t0) cc_final: 0.8191 (t0) REVERT: G 131 MET cc_start: 0.1571 (ptp) cc_final: 0.0753 (mmm) REVERT: H 35 PHE cc_start: 0.7716 (m-80) cc_final: 0.7360 (m-80) REVERT: H 57 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: H 66 GLU cc_start: 0.5471 (OUTLIER) cc_final: 0.3624 (mp0) REVERT: H 76 ASN cc_start: 0.8043 (t0) cc_final: 0.7584 (p0) REVERT: H 81 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8021 (mmp80) REVERT: H 95 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7800 (ptpt) REVERT: H 103 GLU cc_start: 0.8092 (mp0) cc_final: 0.7814 (pm20) REVERT: I 18 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8215 (mm-40) REVERT: I 45 GLN cc_start: 0.8773 (mp10) cc_final: 0.8408 (mp10) REVERT: I 66 THR cc_start: 0.9067 (p) cc_final: 0.8624 (p) REVERT: I 67 GLN cc_start: 0.8790 (pt0) cc_final: 0.8291 (pm20) REVERT: I 69 ILE cc_start: 0.8540 (mm) cc_final: 0.8274 (mm) REVERT: I 71 ASP cc_start: 0.8867 (m-30) cc_final: 0.8365 (m-30) REVERT: I 109 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: K 16 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: K 55 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: L 27 GLU cc_start: 0.8448 (tp30) cc_final: 0.8199 (tp30) REVERT: L 34 ILE cc_start: 0.8466 (mm) cc_final: 0.7913 (mm) REVERT: L 42 ARG cc_start: 0.7810 (mmt-90) cc_final: 0.7192 (mmt-90) REVERT: L 47 LYS cc_start: 0.8726 (tttm) cc_final: 0.8411 (tttt) REVERT: L 56 ASP cc_start: 0.8505 (p0) cc_final: 0.8261 (p0) outliers start: 173 outliers final: 86 residues processed: 514 average time/residue: 0.6439 time to fit residues: 393.9299 Evaluate side-chains 485 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 372 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 984 CYS Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [79, 30, 71, 212, 317, 22, 250, 345, 255, 175, 152] chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 317 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 345 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 723 ASN A1093 GLN A1163 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 123 ASN C 190 ASN D 43 HIS H 130 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078293 restraints weight = 53370.545| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.73 r_work: 0.2917 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32160 Z= 0.140 Angle : 0.577 11.362 43729 Z= 0.292 Chirality : 0.043 0.285 4923 Planarity : 0.004 0.066 5368 Dihedral : 15.084 177.559 5020 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.82 % Allowed : 26.27 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.21 (0.14), residues: 3646 helix: 1.61 (0.15), residues: 1340 sheet: -0.86 (0.24), residues: 471 loop : -0.67 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 255 TYR 0.018 0.001 TYR H 90 PHE 0.025 0.001 PHE C 93 TRP 0.017 0.001 TRP B 236 HIS 0.009 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32134) covalent geometry : angle 0.56197 / 0.29 (43711) hydrogen bonds : bond 0.03740 / 2.50 ( 1328) hydrogen bonds : angle 4.51072 / 3.23 ( 3644) metal coordination : bond 0.00645 / 0.46 ( 26) metal coordination : angle 6.48131 / 4.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 398 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8563 (mm-30) REVERT: A 138 LYS cc_start: 0.7369 (tttt) cc_final: 0.6562 (tptt) REVERT: A 274 ASP cc_start: 0.8128 (t70) cc_final: 0.7370 (t0) REVERT: A 321 GLU cc_start: 0.8735 (pp20) cc_final: 0.8436 (pp20) REVERT: A 329 MET cc_start: 0.8513 (mmm) cc_final: 0.8260 (mmm) REVERT: A 425 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6154 (m-30) REVERT: A 735 GLN cc_start: 0.8209 (mm110) cc_final: 0.7409 (mt0) REVERT: A 740 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: A 853 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5707 (ptpt) REVERT: A 927 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: A 986 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8303 (mtt) REVERT: A 1015 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: A 1094 SER cc_start: 0.8943 (m) cc_final: 0.8568 (p) REVERT: A 1139 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 1160 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8403 (ttm-80) REVERT: A 1207 ILE cc_start: 0.4137 (OUTLIER) cc_final: 0.3794 (tp) REVERT: A 1253 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5925 (pp20) REVERT: A 1255 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 1351 ASP cc_start: 0.8589 (m-30) cc_final: 0.8236 (t0) REVERT: A 1361 ASP cc_start: 0.8714 (t0) cc_final: 0.8186 (t0) REVERT: A 1364 GLU cc_start: 0.8174 (tt0) cc_final: 0.7707 (tt0) REVERT: A 1379 GLU cc_start: 0.8417 (tt0) cc_final: 0.8157 (tt0) REVERT: A 1380 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7560 (mtp180) REVERT: A 1434 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 1441 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7431 (mt-10) REVERT: A 1472 ASP cc_start: 0.8432 (m-30) cc_final: 0.8169 (m-30) REVERT: B 53 MET cc_start: 0.7975 (mpp) cc_final: 0.7166 (mpp) REVERT: B 314 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: B 337 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7618 (tppt) REVERT: B 344 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: B 346 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8215 (mp0) REVERT: B 377 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 436 LYS cc_start: 0.7068 (mttt) cc_final: 0.6867 (mtmt) REVERT: B 555 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7181 (pp20) REVERT: B 584 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8183 (mmt) REVERT: B 609 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8144 (tt0) REVERT: B 645 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: B 681 ASP cc_start: 0.8056 (m-30) cc_final: 0.7682 (m-30) REVERT: B 900 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 1088 GLU cc_start: 0.7559 (tt0) cc_final: 0.6880 (tm-30) REVERT: B 1136 GLU cc_start: 0.7826 (tp30) cc_final: 0.7543 (tm-30) REVERT: B 1143 LYS cc_start: 0.8095 (mptt) cc_final: 0.7695 (tppt) REVERT: C 91 GLU cc_start: 0.8790 (tp30) cc_final: 0.8562 (pp20) REVERT: C 96 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8009 (pp20) REVERT: C 201 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8766 (pm20) REVERT: D 62 MET cc_start: 0.7408 (tpp) cc_final: 0.7043 (tmm) REVERT: D 109 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: E 18 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8392 (mpt) REVERT: E 43 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: E 44 PHE cc_start: 0.8623 (m-80) cc_final: 0.7905 (m-80) REVERT: E 91 CYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8673 (m) REVERT: E 95 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8604 (mm110) REVERT: E 125 TYR cc_start: 0.7543 (m-80) cc_final: 0.6789 (m-10) REVERT: E 177 ASP cc_start: 0.8461 (t0) cc_final: 0.8187 (t0) REVERT: F 61 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8286 (mt-10) REVERT: G 131 MET cc_start: 0.1686 (ptp) cc_final: 0.0827 (mmm) REVERT: H 35 PHE cc_start: 0.7716 (m-80) cc_final: 0.7317 (m-80) REVERT: H 57 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7229 (ttm-80) REVERT: H 65 TYR cc_start: 0.8439 (m-10) cc_final: 0.8183 (m-10) REVERT: H 66 GLU cc_start: 0.5248 (OUTLIER) cc_final: 0.3429 (mp0) REVERT: H 76 ASN cc_start: 0.8050 (t0) cc_final: 0.7596 (p0) REVERT: H 81 ARG cc_start: 0.8484 (mmm160) cc_final: 0.7990 (mmp80) REVERT: H 103 GLU cc_start: 0.8102 (mp0) cc_final: 0.7818 (pm20) REVERT: I 15 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7789 (mpt-90) REVERT: I 18 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8191 (mm-40) REVERT: I 23 MET cc_start: 0.8332 (tpt) cc_final: 0.6931 (ttp) REVERT: I 25 TYR cc_start: 0.6895 (m-80) cc_final: 0.6391 (m-80) REVERT: I 45 GLN cc_start: 0.8874 (mp10) cc_final: 0.8518 (mp10) REVERT: I 66 THR cc_start: 0.9089 (p) cc_final: 0.8644 (p) REVERT: I 67 GLN cc_start: 0.8787 (pt0) cc_final: 0.8288 (pm20) REVERT: I 69 ILE cc_start: 0.8514 (mm) cc_final: 0.8256 (mm) REVERT: I 71 ASP cc_start: 0.8833 (m-30) cc_final: 0.8334 (m-30) REVERT: I 109 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7886 (ttm-80) REVERT: J 57 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8772 (mm-30) REVERT: K 16 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: L 27 GLU cc_start: 0.8421 (tp30) cc_final: 0.8097 (tp30) REVERT: L 34 ILE cc_start: 0.8470 (mm) cc_final: 0.7899 (mm) REVERT: L 42 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7186 (mmt-90) REVERT: L 47 LYS cc_start: 0.8724 (tttm) cc_final: 0.8395 (tttt) outliers start: 159 outliers final: 78 residues processed: 522 average time/residue: 0.6540 time to fit residues: 404.6105 Evaluate side-chains 486 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 378 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [127, 342, 17, 65, 325, 280, 64, 195, 158, 31, 306] chunk 127 optimal weight: 3.9990 chunk 342 optimal weight: 0.0470 chunk 17 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 280 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A1163 HIS B 319 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN D 43 HIS G 60 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.118444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078757 restraints weight = 54722.915| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.65 r_work: 0.2954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32160 Z= 0.134 Angle : 0.576 10.776 43729 Z= 0.291 Chirality : 0.043 0.279 4923 Planarity : 0.004 0.088 5368 Dihedral : 15.040 176.928 5020 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.46 % Allowed : 26.79 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.28 (0.14), residues: 3646 helix: 1.62 (0.15), residues: 1348 sheet: -0.75 (0.24), residues: 464 loop : -0.62 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1138 TYR 0.023 0.001 TYR E 90 PHE 0.026 0.001 PHE C 93 TRP 0.016 0.001 TRP B 236 HIS 0.011 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (32134) covalent geometry : angle 0.56434 / 0.29 (43711) hydrogen bonds : bond 0.03580 / 2.40 ( 1328) hydrogen bonds : angle 4.42833 / 3.17 ( 3644) metal coordination : bond 0.00542 / 0.39 ( 26) metal coordination : angle 5.71490 / 3.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 395 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8560 (mm-30) REVERT: A 138 LYS cc_start: 0.7330 (tttt) cc_final: 0.6539 (tptt) REVERT: A 274 ASP cc_start: 0.8038 (t70) cc_final: 0.7333 (t0) REVERT: A 319 ASP cc_start: 0.7880 (t0) cc_final: 0.7624 (t0) REVERT: A 321 GLU cc_start: 0.8755 (pp20) cc_final: 0.8351 (pp20) REVERT: A 329 MET cc_start: 0.8485 (mmm) cc_final: 0.8221 (mmm) REVERT: A 425 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6087 (m-30) REVERT: A 734 ARG cc_start: 0.6303 (mpt180) cc_final: 0.6025 (mpt180) REVERT: A 735 GLN cc_start: 0.8164 (mm110) cc_final: 0.7361 (mt0) REVERT: A 740 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: A 853 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5688 (ptpt) REVERT: A 927 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: A 986 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: A 1094 SER cc_start: 0.8905 (m) cc_final: 0.8528 (p) REVERT: A 1139 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 1207 ILE cc_start: 0.4069 (OUTLIER) cc_final: 0.3703 (tp) REVERT: A 1221 MET cc_start: 0.7758 (mmm) cc_final: 0.7471 (mmm) REVERT: A 1253 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5882 (pp20) REVERT: A 1255 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7090 (tt) REVERT: A 1351 ASP cc_start: 0.8540 (m-30) cc_final: 0.8177 (t0) REVERT: A 1361 ASP cc_start: 0.8678 (t0) cc_final: 0.8153 (t0) REVERT: A 1364 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 1379 GLU cc_start: 0.8388 (tt0) cc_final: 0.8149 (tt0) REVERT: A 1380 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7509 (mtp180) REVERT: A 1434 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7262 (mt-10) REVERT: A 1472 ASP cc_start: 0.8397 (m-30) cc_final: 0.8137 (m-30) REVERT: B 314 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: B 337 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7502 (tppt) REVERT: B 344 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: B 346 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8216 (mp0) REVERT: B 377 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 442 ASP cc_start: 0.7307 (t70) cc_final: 0.6820 (m-30) REVERT: B 555 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: B 609 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8135 (tt0) REVERT: B 645 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: B 681 ASP cc_start: 0.8057 (m-30) cc_final: 0.7708 (m-30) REVERT: B 900 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: B 1033 THR cc_start: 0.9035 (p) cc_final: 0.8789 (t) REVERT: B 1088 GLU cc_start: 0.7496 (tt0) cc_final: 0.6820 (tm-30) REVERT: B 1136 GLU cc_start: 0.7749 (tp30) cc_final: 0.7441 (tm-30) REVERT: B 1143 LYS cc_start: 0.8117 (mptt) cc_final: 0.7720 (tppt) REVERT: C 6 GLN cc_start: 0.8803 (mp10) cc_final: 0.8469 (mm-40) REVERT: C 91 GLU cc_start: 0.8813 (tp30) cc_final: 0.8572 (pp20) REVERT: C 96 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8116 (pp20) REVERT: C 201 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8761 (pm20) REVERT: D 62 MET cc_start: 0.7345 (tpp) cc_final: 0.6994 (tmm) REVERT: D 109 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5857 (mp0) REVERT: D 119 GLU cc_start: 0.6108 (mm-30) cc_final: 0.5486 (tm-30) REVERT: E 18 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8373 (mpt) REVERT: E 23 ASP cc_start: 0.8617 (m-30) cc_final: 0.8252 (m-30) REVERT: E 43 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8430 (tm-30) REVERT: E 44 PHE cc_start: 0.8593 (m-80) cc_final: 0.7902 (m-80) REVERT: E 88 LYS cc_start: 0.9074 (tptm) cc_final: 0.8611 (mtmt) REVERT: E 91 CYS cc_start: 0.9106 (t) cc_final: 0.8639 (m) REVERT: E 95 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8609 (mm110) REVERT: E 107 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: E 125 TYR cc_start: 0.7462 (m-80) cc_final: 0.6820 (m-10) REVERT: E 177 ASP cc_start: 0.8395 (t0) cc_final: 0.8093 (t0) REVERT: F 61 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8215 (mt-10) REVERT: G 131 MET cc_start: 0.1706 (ptp) cc_final: 0.0860 (mmm) REVERT: H 57 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7175 (ttm-80) REVERT: H 65 TYR cc_start: 0.8383 (m-10) cc_final: 0.8127 (m-10) REVERT: H 66 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.3443 (mp0) REVERT: H 76 ASN cc_start: 0.8010 (t0) cc_final: 0.7555 (p0) REVERT: H 81 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8012 (mmp80) REVERT: H 103 GLU cc_start: 0.8065 (mp0) cc_final: 0.7754 (pm20) REVERT: H 145 MET cc_start: 0.8578 (mtp) cc_final: 0.8309 (mtm) REVERT: I 15 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7574 (mpt-90) REVERT: I 18 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8188 (mm-40) REVERT: I 45 GLN cc_start: 0.8920 (mp10) cc_final: 0.8590 (mp10) REVERT: I 66 THR cc_start: 0.9095 (p) cc_final: 0.8621 (p) REVERT: I 67 GLN cc_start: 0.8756 (pt0) cc_final: 0.8290 (pm20) REVERT: I 69 ILE cc_start: 0.8440 (mm) cc_final: 0.8193 (mm) REVERT: I 71 ASP cc_start: 0.8778 (m-30) cc_final: 0.8327 (m-30) REVERT: I 109 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.8009 (ttm-80) REVERT: K 16 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: K 55 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: L 26 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7881 (m-40) REVERT: L 27 GLU cc_start: 0.8433 (tp30) cc_final: 0.8172 (tp30) REVERT: L 34 ILE cc_start: 0.8391 (mm) cc_final: 0.7814 (mm) REVERT: L 42 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7114 (mmt-90) REVERT: L 47 LYS cc_start: 0.8642 (tttm) cc_final: 0.8316 (tttt) REVERT: L 56 ASP cc_start: 0.8135 (p0) cc_final: 0.7935 (p0) outliers start: 147 outliers final: 81 residues processed: 509 average time/residue: 0.6676 time to fit residues: 403.3175 Evaluate side-chains 496 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 384 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [80, 52, 14, 371, 38, 66, 188, 163, 149, 95, 346] chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 371 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 163 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 GLN A1093 GLN A1163 HIS B 319 ASN B1097 HIS C 5 ASN D 43 HIS H 130 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.116395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076352 restraints weight = 55061.462| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.66 r_work: 0.2917 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 32160 Z= 0.250 Angle : 0.624 11.250 43729 Z= 0.315 Chirality : 0.045 0.287 4923 Planarity : 0.004 0.082 5368 Dihedral : 15.079 177.740 5018 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.43 % Allowed : 26.85 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.19 (0.14), residues: 3646 helix: 1.52 (0.15), residues: 1345 sheet: -0.81 (0.24), residues: 464 loop : -0.65 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 9 TYR 0.016 0.002 TYR H 90 PHE 0.030 0.002 PHE C 93 TRP 0.027 0.001 TRP B 236 HIS 0.012 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (32134) covalent geometry : angle 0.61218 / 0.31 (43711) hydrogen bonds : bond 0.03966 / 2.65 ( 1328) hydrogen bonds : angle 4.52462 / 3.24 ( 3644) metal coordination : bond 0.00704 / 0.47 ( 26) metal coordination : angle 5.98672 / 3.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 378 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8559 (mm-30) REVERT: A 138 LYS cc_start: 0.7349 (tttt) cc_final: 0.6537 (tptt) REVERT: A 274 ASP cc_start: 0.8080 (t70) cc_final: 0.7413 (t0) REVERT: A 319 ASP cc_start: 0.7947 (t0) cc_final: 0.7732 (t0) REVERT: A 321 GLU cc_start: 0.8736 (pp20) cc_final: 0.8397 (pp20) REVERT: A 329 MET cc_start: 0.8462 (mmm) cc_final: 0.8236 (mmm) REVERT: A 425 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.6172 (m-30) REVERT: A 483 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8078 (mtm180) REVERT: A 556 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: A 735 GLN cc_start: 0.8184 (mm110) cc_final: 0.7370 (mt0) REVERT: A 740 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: A 853 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.5689 (ptpt) REVERT: A 927 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: A 986 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: A 1094 SER cc_start: 0.8937 (m) cc_final: 0.8556 (p) REVERT: A 1207 ILE cc_start: 0.4081 (OUTLIER) cc_final: 0.3696 (tp) REVERT: A 1253 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5890 (pp20) REVERT: A 1255 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7112 (tt) REVERT: A 1351 ASP cc_start: 0.8606 (m-30) cc_final: 0.8239 (t0) REVERT: A 1361 ASP cc_start: 0.8728 (t0) cc_final: 0.8184 (t0) REVERT: A 1364 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: A 1379 GLU cc_start: 0.8343 (tt0) cc_final: 0.8106 (tt0) REVERT: A 1380 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: A 1434 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 1441 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 1472 ASP cc_start: 0.8393 (m-30) cc_final: 0.8086 (m-30) REVERT: B 314 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: B 337 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7533 (tppt) REVERT: B 344 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: B 346 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8265 (mp0) REVERT: B 555 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: B 645 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: B 681 ASP cc_start: 0.8123 (m-30) cc_final: 0.7744 (m-30) REVERT: B 900 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: B 1088 GLU cc_start: 0.7595 (tt0) cc_final: 0.6898 (tm-30) REVERT: B 1136 GLU cc_start: 0.7792 (tp30) cc_final: 0.7471 (tm-30) REVERT: B 1143 LYS cc_start: 0.8051 (mptt) cc_final: 0.7627 (tppt) REVERT: C 91 GLU cc_start: 0.8842 (tp30) cc_final: 0.8574 (pp20) REVERT: C 96 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8006 (pp20) REVERT: C 201 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: D 62 MET cc_start: 0.7353 (tpp) cc_final: 0.7001 (tmm) REVERT: D 119 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5449 (tm-30) REVERT: E 18 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8364 (mpt) REVERT: E 23 ASP cc_start: 0.8645 (m-30) cc_final: 0.8310 (m-30) REVERT: E 43 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: E 44 PHE cc_start: 0.8589 (m-80) cc_final: 0.7881 (m-80) REVERT: E 73 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6248 (t80) REVERT: E 88 LYS cc_start: 0.9072 (tptm) cc_final: 0.8599 (mtmt) REVERT: E 91 CYS cc_start: 0.9124 (t) cc_final: 0.8698 (m) REVERT: E 95 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8720 (mm-40) REVERT: E 107 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: E 158 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: E 177 ASP cc_start: 0.8400 (t0) cc_final: 0.8138 (t0) REVERT: G 131 MET cc_start: 0.1742 (ptp) cc_final: 0.0818 (mmm) REVERT: H 57 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7210 (ttm-80) REVERT: H 65 TYR cc_start: 0.8433 (m-10) cc_final: 0.8168 (m-10) REVERT: H 66 GLU cc_start: 0.5264 (OUTLIER) cc_final: 0.3472 (mp0) REVERT: H 76 ASN cc_start: 0.8027 (t0) cc_final: 0.7552 (p0) REVERT: H 81 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8005 (mmp80) REVERT: H 92 MET cc_start: 0.8911 (mtp) cc_final: 0.8678 (mtp) REVERT: H 103 GLU cc_start: 0.8077 (mp0) cc_final: 0.7808 (pm20) REVERT: H 145 MET cc_start: 0.8583 (mtp) cc_final: 0.8317 (mtm) REVERT: I 15 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7644 (mpt-90) REVERT: I 18 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8227 (mm-40) REVERT: I 45 GLN cc_start: 0.8863 (mp10) cc_final: 0.8497 (mp-120) REVERT: I 66 THR cc_start: 0.9050 (p) cc_final: 0.8618 (p) REVERT: I 67 GLN cc_start: 0.8758 (pt0) cc_final: 0.8274 (pm20) REVERT: I 69 ILE cc_start: 0.8509 (mm) cc_final: 0.8238 (mm) REVERT: I 71 ASP cc_start: 0.8797 (m-30) cc_final: 0.8374 (m-30) REVERT: I 109 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: J 19 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: K 16 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: K 55 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: L 27 GLU cc_start: 0.8462 (tp30) cc_final: 0.8140 (tp30) REVERT: L 34 ILE cc_start: 0.8412 (mm) cc_final: 0.8197 (mm) REVERT: L 42 ARG cc_start: 0.7813 (mmt-90) cc_final: 0.7301 (mmt-90) REVERT: L 47 LYS cc_start: 0.8630 (tttm) cc_final: 0.8318 (tttt) REVERT: L 56 ASP cc_start: 0.8219 (p0) cc_final: 0.7976 (p0) outliers start: 146 outliers final: 83 residues processed: 494 average time/residue: 0.6804 time to fit residues: 397.1779 Evaluate side-chains 486 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 371 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 55 GLN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [54, 77, 33, 316, 98, 248, 176, 35, 70, 291, 373] chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A1163 HIS C 5 ASN G 60 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078084 restraints weight = 54694.719| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.65 r_work: 0.2951 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32160 Z= 0.145 Angle : 0.594 13.918 43729 Z= 0.299 Chirality : 0.043 0.283 4923 Planarity : 0.004 0.077 5368 Dihedral : 15.058 176.874 5016 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 3.79 % Allowed : 27.70 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.27 (0.14), residues: 3646 helix: 1.59 (0.15), residues: 1343 sheet: -0.73 (0.24), residues: 455 loop : -0.61 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 9 TYR 0.014 0.001 TYR H 142 PHE 0.033 0.001 PHE C 93 TRP 0.025 0.001 TRP B 236 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (32134) covalent geometry : angle 0.58355 / 0.30 (43711) hydrogen bonds : bond 0.03624 / 2.43 ( 1328) hydrogen bonds : angle 4.44026 / 3.18 ( 3644) metal coordination : bond 0.00495 / 0.34 ( 26) metal coordination : angle 5.46604 / 3.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 384 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8544 (mm-30) REVERT: A 138 LYS cc_start: 0.7332 (tttt) cc_final: 0.6528 (tptt) REVERT: A 238 MET cc_start: 0.8067 (mpp) cc_final: 0.7706 (mtt) REVERT: A 274 ASP cc_start: 0.8038 (t70) cc_final: 0.7329 (t0) REVERT: A 319 ASP cc_start: 0.7935 (t0) cc_final: 0.7730 (t0) REVERT: A 321 GLU cc_start: 0.8709 (pp20) cc_final: 0.8358 (pp20) REVERT: A 329 MET cc_start: 0.8484 (mmm) cc_final: 0.8254 (mmm) REVERT: A 425 ASP cc_start: 0.6473 (OUTLIER) cc_final: 0.6146 (m-30) REVERT: A 520 MET cc_start: 0.8167 (mmm) cc_final: 0.7940 (mmp) REVERT: A 556 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: A 715 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: A 734 ARG cc_start: 0.6308 (mpt180) cc_final: 0.6061 (mpt180) REVERT: A 735 GLN cc_start: 0.8166 (mm110) cc_final: 0.7349 (mt0) REVERT: A 740 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: A 853 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5668 (ptpt) REVERT: A 927 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: A 986 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8249 (mtt) REVERT: A 1094 SER cc_start: 0.8905 (m) cc_final: 0.8525 (p) REVERT: A 1207 ILE cc_start: 0.4080 (OUTLIER) cc_final: 0.3687 (tp) REVERT: A 1253 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5887 (pp20) REVERT: A 1255 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 1351 ASP cc_start: 0.8549 (m-30) cc_final: 0.8183 (t0) REVERT: A 1361 ASP cc_start: 0.8712 (t0) cc_final: 0.8198 (t0) REVERT: A 1364 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 1379 GLU cc_start: 0.8336 (tt0) cc_final: 0.8093 (tt0) REVERT: A 1380 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: A 1434 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7343 (mt-10) REVERT: A 1472 ASP cc_start: 0.8488 (m-30) cc_final: 0.8238 (m-30) REVERT: B 337 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7499 (tppt) REVERT: B 344 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: B 346 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8236 (mp0) REVERT: B 377 LEU cc_start: 0.8364 (mt) cc_final: 0.8164 (mp) REVERT: B 442 ASP cc_start: 0.7305 (t70) cc_final: 0.6822 (m-30) REVERT: B 497 LYS cc_start: 0.7908 (pptt) cc_final: 0.7666 (pptt) REVERT: B 555 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: B 645 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: B 681 ASP cc_start: 0.8066 (m-30) cc_final: 0.7690 (m-30) REVERT: B 900 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: B 1033 THR cc_start: 0.9041 (p) cc_final: 0.8790 (t) REVERT: B 1088 GLU cc_start: 0.7501 (tt0) cc_final: 0.6830 (tm-30) REVERT: B 1136 GLU cc_start: 0.7718 (tp30) cc_final: 0.7375 (tm-30) REVERT: B 1143 LYS cc_start: 0.8040 (mptt) cc_final: 0.7607 (tppt) REVERT: C 6 GLN cc_start: 0.8834 (mp10) cc_final: 0.8488 (mm-40) REVERT: C 91 GLU cc_start: 0.8855 (tp30) cc_final: 0.8600 (pp20) REVERT: C 96 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: C 201 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: D 62 MET cc_start: 0.7342 (tpp) cc_final: 0.6981 (tmm) REVERT: D 109 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: D 119 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5410 (tm-30) REVERT: E 18 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8354 (mpt) REVERT: E 23 ASP cc_start: 0.8624 (m-30) cc_final: 0.8277 (m-30) REVERT: E 43 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: E 44 PHE cc_start: 0.8576 (m-80) cc_final: 0.7876 (m-80) REVERT: E 88 LYS cc_start: 0.9060 (tptm) cc_final: 0.8590 (mtmt) REVERT: E 91 CYS cc_start: 0.9082 (t) cc_final: 0.8728 (m) REVERT: E 107 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: E 125 TYR cc_start: 0.7389 (m-80) cc_final: 0.7180 (m-10) REVERT: E 158 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: E 177 ASP cc_start: 0.8399 (t0) cc_final: 0.8108 (t0) REVERT: F 61 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8218 (mt-10) REVERT: G 24 ASN cc_start: 0.8332 (m110) cc_final: 0.7892 (m-40) REVERT: G 28 GLN cc_start: 0.7917 (tt0) cc_final: 0.7590 (mt0) REVERT: G 131 MET cc_start: 0.1774 (ptp) cc_final: 0.0855 (mmm) REVERT: H 57 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7153 (ttm-80) REVERT: H 65 TYR cc_start: 0.8401 (m-10) cc_final: 0.8140 (m-10) REVERT: H 66 GLU cc_start: 0.5113 (OUTLIER) cc_final: 0.3365 (mp0) REVERT: H 76 ASN cc_start: 0.8022 (t0) cc_final: 0.7570 (p0) REVERT: H 81 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8026 (mmp80) REVERT: H 103 GLU cc_start: 0.8056 (mp0) cc_final: 0.7807 (pm20) REVERT: I 15 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7673 (mpt-90) REVERT: I 18 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8178 (mm-40) REVERT: I 45 GLN cc_start: 0.8923 (mp10) cc_final: 0.8576 (mp10) REVERT: I 66 THR cc_start: 0.9082 (p) cc_final: 0.8611 (p) REVERT: I 67 GLN cc_start: 0.8788 (pt0) cc_final: 0.8323 (pm20) REVERT: I 69 ILE cc_start: 0.8459 (mm) cc_final: 0.8184 (mm) REVERT: I 71 ASP cc_start: 0.8775 (m-30) cc_final: 0.8331 (m-30) REVERT: I 109 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7832 (ttm-80) REVERT: K 16 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: L 26 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8003 (t0) REVERT: L 27 GLU cc_start: 0.8476 (tp30) cc_final: 0.8198 (tp30) REVERT: L 34 ILE cc_start: 0.8385 (mm) cc_final: 0.8154 (mm) REVERT: L 42 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7325 (mmt-90) REVERT: L 47 LYS cc_start: 0.8639 (tttm) cc_final: 0.8315 (tttt) REVERT: L 56 ASP cc_start: 0.8268 (p0) cc_final: 0.8039 (p0) outliers start: 125 outliers final: 81 residues processed: 486 average time/residue: 0.6651 time to fit residues: 383.2565 Evaluate side-chains 489 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 379 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1364 GLU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [96, 48, 251, 20, 123, 63, 135, 300, 162, 154, 240] chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 123 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 300 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 HIS A 673 GLN A1093 GLN A1163 HIS C 5 ASN H 130 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079049 restraints weight = 54670.077| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.65 r_work: 0.2966 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32160 Z= 0.122 Angle : 0.589 14.480 43729 Z= 0.298 Chirality : 0.043 0.279 4923 Planarity : 0.004 0.076 5368 Dihedral : 15.025 176.349 5016 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 3.52 % Allowed : 28.09 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 3646 helix: 1.66 (0.15), residues: 1334 sheet: -0.69 (0.24), residues: 457 loop : -0.57 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 438 TYR 0.020 0.001 TYR H 90 PHE 0.036 0.001 PHE C 93 TRP 0.025 0.001 TRP B 236 HIS 0.007 0.001 HIS B 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (32134) covalent geometry : angle 0.58052 / 0.30 (43711) hydrogen bonds : bond 0.03497 / 2.35 ( 1328) hydrogen bonds : angle 4.38757 / 3.14 ( 3644) metal coordination : bond 0.00398 / 0.28 ( 26) metal coordination : angle 4.95059 / 3.13 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 389 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8547 (mm-30) REVERT: A 138 LYS cc_start: 0.7360 (tttt) cc_final: 0.6532 (tptt) REVERT: A 238 MET cc_start: 0.8077 (mpp) cc_final: 0.7517 (mtm) REVERT: A 274 ASP cc_start: 0.8009 (t70) cc_final: 0.7300 (t0) REVERT: A 319 ASP cc_start: 0.7922 (t0) cc_final: 0.7722 (t0) REVERT: A 321 GLU cc_start: 0.8689 (pp20) cc_final: 0.8326 (pp20) REVERT: A 329 MET cc_start: 0.8456 (mmm) cc_final: 0.8227 (mmm) REVERT: A 425 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.6209 (m-30) REVERT: A 520 MET cc_start: 0.8138 (mmm) cc_final: 0.7911 (mmp) REVERT: A 556 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: A 715 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: A 734 ARG cc_start: 0.6317 (mpt180) cc_final: 0.6071 (mpt180) REVERT: A 735 GLN cc_start: 0.8169 (mm110) cc_final: 0.7358 (mt0) REVERT: A 740 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: A 853 LYS cc_start: 0.6476 (OUTLIER) cc_final: 0.5627 (ptpt) REVERT: A 927 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: A 986 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8234 (mtt) REVERT: A 1094 SER cc_start: 0.8898 (m) cc_final: 0.8516 (p) REVERT: A 1207 ILE cc_start: 0.4136 (OUTLIER) cc_final: 0.3734 (tp) REVERT: A 1253 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5890 (pp20) REVERT: A 1351 ASP cc_start: 0.8521 (m-30) cc_final: 0.8155 (t0) REVERT: A 1361 ASP cc_start: 0.8693 (t0) cc_final: 0.8152 (t0) REVERT: A 1364 GLU cc_start: 0.8105 (tt0) cc_final: 0.7663 (tt0) REVERT: A 1379 GLU cc_start: 0.8356 (tt0) cc_final: 0.8119 (tt0) REVERT: A 1380 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7507 (mtp180) REVERT: A 1434 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 314 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: B 337 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7492 (tppt) REVERT: B 344 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: B 346 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8237 (mp0) REVERT: B 377 LEU cc_start: 0.8370 (mt) cc_final: 0.8161 (mp) REVERT: B 442 ASP cc_start: 0.7284 (t70) cc_final: 0.6803 (m-30) REVERT: B 497 LYS cc_start: 0.7893 (pptt) cc_final: 0.7636 (pptt) REVERT: B 555 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: B 609 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8021 (tt0) REVERT: B 645 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: B 681 ASP cc_start: 0.8068 (m-30) cc_final: 0.7696 (m-30) REVERT: B 900 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: B 1033 THR cc_start: 0.9030 (p) cc_final: 0.8788 (t) REVERT: B 1088 GLU cc_start: 0.7473 (tt0) cc_final: 0.6820 (tm-30) REVERT: B 1136 GLU cc_start: 0.7707 (tp30) cc_final: 0.7332 (tm-30) REVERT: B 1143 LYS cc_start: 0.8071 (mptt) cc_final: 0.7675 (tppt) REVERT: C 91 GLU cc_start: 0.8874 (tp30) cc_final: 0.8609 (pp20) REVERT: C 96 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: C 201 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: D 62 MET cc_start: 0.7307 (tpp) cc_final: 0.6948 (tmm) REVERT: D 109 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5875 (mp0) REVERT: E 18 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8358 (mpt) REVERT: E 23 ASP cc_start: 0.8605 (m-30) cc_final: 0.8251 (m-30) REVERT: E 43 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: E 44 PHE cc_start: 0.8566 (m-80) cc_final: 0.7880 (m-80) REVERT: E 88 LYS cc_start: 0.9072 (tptm) cc_final: 0.8585 (mtmt) REVERT: E 91 CYS cc_start: 0.9076 (t) cc_final: 0.8671 (m) REVERT: E 95 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8686 (mm-40) REVERT: E 107 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: E 158 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: E 177 ASP cc_start: 0.8382 (t0) cc_final: 0.8109 (t0) REVERT: F 61 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8209 (mt-10) REVERT: G 24 ASN cc_start: 0.8353 (m110) cc_final: 0.7903 (m-40) REVERT: G 28 GLN cc_start: 0.7907 (tt0) cc_final: 0.7592 (mt0) REVERT: G 131 MET cc_start: 0.1767 (ptp) cc_final: 0.0861 (mmm) REVERT: H 57 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7060 (ttm-80) REVERT: H 65 TYR cc_start: 0.8344 (m-10) cc_final: 0.8091 (m-10) REVERT: H 66 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.3401 (mp0) REVERT: H 76 ASN cc_start: 0.8044 (t0) cc_final: 0.7608 (p0) REVERT: H 81 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8035 (mmp80) REVERT: H 103 GLU cc_start: 0.8039 (mp0) cc_final: 0.7725 (pm20) REVERT: I 15 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7663 (mpt-90) REVERT: I 18 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8198 (mm-40) REVERT: I 45 GLN cc_start: 0.8907 (mp10) cc_final: 0.8562 (mp10) REVERT: I 66 THR cc_start: 0.9096 (p) cc_final: 0.8647 (p) REVERT: I 67 GLN cc_start: 0.8783 (pt0) cc_final: 0.8325 (pm20) REVERT: I 69 ILE cc_start: 0.8442 (mm) cc_final: 0.8190 (mm) REVERT: I 71 ASP cc_start: 0.8779 (m-30) cc_final: 0.8325 (m-30) REVERT: I 109 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: K 16 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: L 16 ILE cc_start: 0.8730 (mm) cc_final: 0.8394 (mm) REVERT: L 27 GLU cc_start: 0.8470 (tp30) cc_final: 0.8238 (tp30) REVERT: L 28 ILE cc_start: 0.8759 (mm) cc_final: 0.8493 (mp) REVERT: L 34 ILE cc_start: 0.8352 (mm) cc_final: 0.8096 (mm) REVERT: L 42 ARG cc_start: 0.7741 (mmt-90) cc_final: 0.7312 (mmt-90) REVERT: L 47 LYS cc_start: 0.8648 (tttm) cc_final: 0.8273 (tttt) REVERT: L 56 ASP cc_start: 0.8292 (p0) cc_final: 0.8060 (p0) outliers start: 116 outliers final: 75 residues processed: 484 average time/residue: 0.6763 time to fit residues: 387.0717 Evaluate side-chains 479 residues out of total 3314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 376 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 41 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: [320, 113, 98, 146, 89, 331, 358, 72, 109, 212, 121] chunk 320 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 358 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 109 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1163 HIS B 52 GLN C 5 ASN ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078790 restraints weight = 54864.287| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.65 r_work: 0.2962 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32160 Z= 0.144 Angle : 0.590 11.223 43729 Z= 0.298 Chirality : 0.043 0.280 4923 Planarity : 0.004 0.076 5368 Dihedral : 14.973 176.312 5011 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 3.43 % Allowed : 28.28 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.35 (0.14), residues: 3646 helix: 1.66 (0.15), residues: 1334 sheet: -0.68 (0.24), residues: 457 loop : -0.56 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 9 TYR 0.018 0.001 TYR C 164 PHE 0.040 0.001 PHE C 93 TRP 0.024 0.001 TRP B 236 HIS 0.007 0.001 HIS B 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (32134) covalent geometry : angle 0.58225 / 0.30 (43711) hydrogen bonds : bond 0.03521 / 2.37 ( 1328) hydrogen bonds : angle 4.36523 / 3.12 ( 3644) metal coordination : bond 0.00425 / 0.29 ( 26) metal coordination : angle 4.79048 / 3.04 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12781.11 seconds wall clock time: 217 minutes 36.51 seconds (13056.51 seconds total)