Starting phenix.real_space_refine on Thu Oct 29 15:33:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ycz_72792/10_2026/9ycz_72792.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ycz_72792/10_2026/9ycz_72792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ycz_72792/10_2026/9ycz_72792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ycz_72792/10_2026/9ycz_72792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ycz_72792/10_2026/9ycz_72792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ycz_72792/10_2026/9ycz_72792.map" } resolution = 2.9 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 80 5.49 5 Mg 1 5.21 5 S 195 5.16 5 C 19934 2.51 5 N 5587 2.21 5 O 6142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 31947 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10950 Classifications: {'peptide': 1379} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1310} Chain breaks: 12 Chain: "B" Number of atoms: 8739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8739 Classifications: {'peptide': 1092} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1040} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2038 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 15, 'TRANS': 238} 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: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} 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: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 877 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 2 Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "P" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 340 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 758 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} 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 71 106.435 82.654 75.586 1.00175.57 S ATOM 486 SG CYS A 74 108.699 80.293 75.646 1.00167.63 S ATOM 533 SG CYS A 81 106.064 79.830 75.527 1.00155.55 S ATOM 768 SG CYS A 111 97.711 70.503 122.337 1.00219.00 S ATOM 796 SG CYS A 114 100.246 69.669 123.197 1.00230.76 S ATOM 1055 SG CYS A 154 96.288 68.352 122.159 1.00231.27 S ATOM 19259 SG CYS B1119 108.059 64.920 85.217 1.00177.20 S ATOM 19281 SG CYS B1122 106.941 66.752 87.539 1.00172.74 S ATOM 19396 SG CYS B1137 108.838 68.942 85.963 1.00197.08 S ATOM 20383 SG CYS C 88 73.040 91.852 17.669 1.00186.04 S ATOM 20396 SG CYS C 90 75.384 93.275 20.662 1.00212.43 S ATOM 20431 SG CYS C 94 73.449 95.080 18.182 1.00197.04 S ATOM 20453 SG CYS C 97 71.907 93.532 19.549 1.00206.88 S ATOM 28165 SG CYS I 86 13.050 98.972 105.794 1.00189.33 S ATOM 28189 SG CYS I 89 12.233 101.810 104.963 1.00203.85 S ATOM 28376 SG CYS I 114 14.436 101.587 102.750 1.00189.26 S ATOM 28411 SG CYS I 119 14.244 102.549 106.199 1.00188.77 S ATOM 27636 SG CYS I 17 43.557 104.074 137.393 1.00202.07 S ATOM 27660 SG CYS I 20 46.730 104.438 136.538 1.00207.35 S ATOM 27821 SG CYS I 39 46.066 102.004 136.337 1.00226.54 S ATOM 27846 SG CYS I 42 46.878 104.142 139.930 1.00217.55 S ATOM 28521 SG CYS J 7 46.871 94.747 39.818 1.00135.55 S ATOM 28545 SG CYS J 10 46.555 93.781 37.404 1.00131.38 S ATOM 28809 SG CYS J 44 43.823 92.573 39.062 1.00148.57 S ATOM 28815 SG CYS J 45 43.567 95.725 37.045 1.00142.55 S ATOM 29961 SG CYS L 19 75.891 125.688 53.527 1.00185.93 S ATOM 29980 SG CYS L 22 74.421 129.314 52.549 1.00200.37 S ATOM 30097 SG CYS L 36 78.272 127.276 52.657 1.00191.71 S Time building chain proxies: 6.12, per 1000 atoms: 0.19 Number of scatterers: 31947 At special positions: 0 Unit cell: (172.62, 152.892, 158.646, 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 195 16.00 P 80 15.00 Mg 1 11.99 O 6142 8.00 N 5587 7.00 C 19934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " 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 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 27 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7152 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 46 sheets defined 38.5% alpha, 17.2% beta 32 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.980A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.774A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.749A pdb=" N LYS A 344 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' 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 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.750A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.802A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.704A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.542A 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: 3.540A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.611A 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 759 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: 3.898A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 868 removed outlier: 3.574A pdb=" N THR A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.584A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.553A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.871A 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 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.521A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 removed outlier: 3.926A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.641A 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 1192 through 1197 Processing helix chain 'A' and resid 1227 through 1238 Processing helix chain 'A' and resid 1281 through 1293 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.868A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.554A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1459 removed outlier: 3.912A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1481 removed outlier: 4.298A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.251A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.536A 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 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.549A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 358 through 377 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 424 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.717A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.605A 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: 3.743A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.559A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.112A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.757A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.626A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.783A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.782A pdb=" N ILE B1011 " --> pdb=" O ASN B1007 " (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 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.609A 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: 3.640A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.637A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (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 268 Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.768A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.790A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.513A 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 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.749A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.748A pdb=" N LEU E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 removed outlier: 5.786A 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 166 through 170 Processing helix chain 'E' and resid 177 through 183 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 'I' and resid 64 through 68 Processing helix chain 'I' and resid 70 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.829A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.619A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.956A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.024A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.344A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.752A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.638A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.240A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.831A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB1, first strand: chain 'A' and resid 1335 through 1336 Processing sheet with id=AB2, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 7.332A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1215 through 1216 removed outlier: 3.545A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A1244 " --> pdb=" O ARG A1260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1215 through 1216 removed outlier: 3.545A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1321 through 1322 Processing sheet with id=AB6, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 93 removed outlier: 6.589A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.859A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.491A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.948A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.948A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.112A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 828 through 829 Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.099A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD5, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 9 removed outlier: 4.322A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 121 through 122 removed outlier: 7.129A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.709A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.672A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR G 37 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.672A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL G 58 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.756A 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: 3.819A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.140A 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 139 through 143 removed outlier: 3.769A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 29 removed outlier: 4.061A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) 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 19 through 23 1299 hydrogen bonds defined for protein. 3558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 9.86 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10127 1.33 - 1.46: 5607 1.46 - 1.58: 16495 1.58 - 1.70: 156 1.70 - 1.82: 308 Bond restraints: 32693 Sorted by residual: bond pdb=" C CYS C 90 " pdb=" N GLU C 91 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.39e-02 5.18e+03 1.09e+01 bond pdb=" C1' DC T 38 " pdb=" N1 DC T 38 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.46e+00 bond pdb=" C1' DT T 11 " pdb=" N1 DT T 11 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 7.97e+00 bond pdb=" C3' DG T 27 " pdb=" O3' DG T 27 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 7.91e+00 bond pdb=" N VAL J 14 " pdb=" CA VAL J 14 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.09e-02 8.42e+03 7.46e+00 ... (remaining 32688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.92: 44485 7.92 - 15.85: 5 15.85 - 23.77: 2 23.77 - 31.69: 0 31.69 - 39.62: 1 Bond angle restraints: 44493 Sorted by residual: angle pdb=" C CYS C 90 " pdb=" CA CYS C 90 " pdb=" CB CYS C 90 " ideal model delta sigma weight residual 110.19 70.57 39.62 2.18e+00 2.10e-01 3.30e+02 angle pdb=" N CYS A 74 " pdb=" CA CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sigma weight residual 110.60 91.53 19.07 1.52e+00 4.33e-01 1.57e+02 angle pdb=" C CYS C 97 " pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sigma weight residual 110.42 127.33 -16.91 1.99e+00 2.53e-01 7.22e+01 angle pdb=" C CYS A 154 " pdb=" CA CYS A 154 " pdb=" CB CYS A 154 " ideal model delta sigma weight residual 110.85 97.71 13.14 1.70e+00 3.46e-01 5.98e+01 angle pdb=" C THR C 89 " pdb=" N CYS C 90 " pdb=" CA CYS C 90 " ideal model delta sigma weight residual 121.06 108.74 12.32 1.88e+00 2.83e-01 4.29e+01 ... (remaining 44488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 18711 35.72 - 71.44: 1110 71.44 - 107.16: 54 107.16 - 142.88: 0 142.88 - 178.60: 3 Dihedral angle restraints: 19878 sinusoidal: 8844 harmonic: 11034 Sorted by residual: dihedral pdb=" C CYS C 90 " pdb=" N CYS C 90 " pdb=" CA CYS C 90 " pdb=" CB CYS C 90 " ideal model delta harmonic sigma weight residual -122.60 -77.19 -45.41 0 2.50e+00 1.60e-01 3.30e+02 dihedral pdb=" N CYS A 74 " pdb=" C CYS A 74 " pdb=" CA CYS A 74 " pdb=" CB CYS A 74 " ideal model delta harmonic sigma weight residual 122.80 98.86 23.94 0 2.50e+00 1.60e-01 9.17e+01 dihedral pdb=" C CYS C 97 " pdb=" N CYS C 97 " pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " ideal model delta harmonic sigma weight residual -122.60 -139.06 16.46 0 2.50e+00 1.60e-01 4.33e+01 ... (remaining 19875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4624 0.094 - 0.187: 371 0.187 - 0.281: 12 0.281 - 0.375: 0 0.375 - 0.468: 2 Chirality restraints: 5009 Sorted by residual: chirality pdb=" CA CYS C 97 " pdb=" N CYS C 97 " pdb=" C CYS C 97 " pdb=" CB CYS C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA CYS A 74 " pdb=" N CYS A 74 " pdb=" C CYS A 74 " pdb=" CB CYS A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA VAL J 14 " pdb=" N VAL J 14 " pdb=" C VAL J 14 " pdb=" CB VAL J 14 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 5006 not shown) Planarity restraints: 5469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 96 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C GLU C 96 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU C 96 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS C 97 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1214 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C VAL A1214 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL A1214 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A1215 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 73 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C THR A 73 " 0.050 2.00e-02 2.50e+03 pdb=" O THR A 73 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 74 " -0.017 2.00e-02 2.50e+03 ... (remaining 5466 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 7 2.19 - 2.87: 11996 2.87 - 3.55: 45239 3.55 - 4.22: 76600 4.22 - 4.90: 134648 Nonbonded interactions: 268490 Sorted by model distance: nonbonded pdb=" OD2 ASP A 495 " pdb="MG MG A2003 " model vdw 1.517 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.684 2.170 nonbonded pdb=" CG ASP A 495 " pdb="MG MG A2003 " model vdw 1.736 2.400 nonbonded pdb=" OP1 C P 47 " pdb="MG MG A2003 " model vdw 2.002 2.170 nonbonded pdb=" CB CYS A 71 " pdb=" SG CYS A 74 " model vdw 2.024 3.040 ... (remaining 268485 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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.830 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.007 0.535 32722 Z= 0.321 Angle : 0.928 48.025 44520 Z= 0.407 Chirality : 0.047 0.468 5009 Planarity : 0.004 0.062 5469 Dihedral : 19.774 178.596 12726 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.40 % Allowed : 30.88 % Favored : 67.71 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.10 % 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: -0.61 (0.14), residues: 3717 helix: 1.20 (0.15), residues: 1299 sheet: -1.88 (0.21), residues: 539 loop : -1.07 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 16 TYR 0.018 0.001 TYR I 54 PHE 0.022 0.001 PHE A 496 TRP 0.011 0.001 TRP C 49 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.26 (32693) covalent geometry : angle 0.64449 / 0.39 (44493) hydrogen bonds : bond 0.13403 / 9.09 ( 1347) hydrogen bonds : angle 6.78842 / 4.79 ( 3726) metal coordination : bond 0.18841 / 11.10 ( 29) metal coordination : angle 27.11731 / 18.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 392 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7900 (mp0) REVERT: A 119 VAL cc_start: 0.8167 (p) cc_final: 0.7864 (m) REVERT: A 238 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7059 (mtm) REVERT: A 266 MET cc_start: 0.4052 (pp-130) cc_final: 0.3598 (pp-130) REVERT: A 426 ARG cc_start: 0.8408 (tpp80) cc_final: 0.7838 (ttm-80) REVERT: A 734 ARG cc_start: 0.7055 (mpt-90) cc_final: 0.6659 (mpp-170) REVERT: A 762 GLU cc_start: 0.8600 (pm20) cc_final: 0.8297 (pm20) REVERT: A 861 GLN cc_start: 0.8402 (mt0) cc_final: 0.8085 (mt0) REVERT: A 1189 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6361 (p0) REVERT: A 1215 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7724 (pp20) REVERT: A 1303 GLN cc_start: 0.8184 (mp10) cc_final: 0.7806 (mp10) REVERT: A 1331 LEU cc_start: 0.7858 (mt) cc_final: 0.7554 (pt) REVERT: A 1383 TYR cc_start: 0.8192 (t80) cc_final: 0.7919 (t80) REVERT: A 1441 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: B 36 GLU cc_start: 0.8791 (tp30) cc_final: 0.8400 (tp30) REVERT: B 49 GLU cc_start: 0.7695 (tp30) cc_final: 0.7439 (tp30) REVERT: B 53 MET cc_start: 0.7995 (mpt) cc_final: 0.7792 (mpt) REVERT: B 298 MET cc_start: 0.8664 (mpp) cc_final: 0.7878 (mtm) REVERT: B 344 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: B 420 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5684 (tp-100) REVERT: B 497 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7227 (pttp) REVERT: B 1026 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 1028 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 1080 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8272 (mtt180) REVERT: E 9 ARG cc_start: 0.8080 (mpt-90) cc_final: 0.7750 (mtm-85) REVERT: E 121 MET cc_start: 0.7661 (ttp) cc_final: 0.7363 (ttm) REVERT: E 137 ILE cc_start: 0.8615 (pp) cc_final: 0.8305 (pp) REVERT: F 84 GLU cc_start: 0.8252 (pm20) cc_final: 0.7874 (pm20) REVERT: F 86 GLU cc_start: 0.7803 (mp0) cc_final: 0.6777 (mp0) REVERT: G 1 MET cc_start: 0.7922 (mpp) cc_final: 0.7505 (mmm) REVERT: H 47 ILE cc_start: 0.8559 (tt) cc_final: 0.8312 (tt) REVERT: H 89 GLU cc_start: 0.8313 (pt0) cc_final: 0.8006 (pt0) REVERT: H 103 GLU cc_start: 0.8400 (pm20) cc_final: 0.8149 (pm20) REVERT: H 136 GLU cc_start: 0.7771 (pt0) cc_final: 0.7258 (pm20) REVERT: I 33 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7239 (ttm-80) REVERT: J 30 THR cc_start: 0.8983 (m) cc_final: 0.8656 (p) REVERT: J 36 ASP cc_start: 0.8814 (m-30) cc_final: 0.8500 (m-30) REVERT: K 24 ASP cc_start: 0.7644 (t0) cc_final: 0.7322 (t0) REVERT: K 38 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8368 (mm-30) REVERT: K 68 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7890 (mt-10) REVERT: K 75 VAL cc_start: 0.8994 (t) cc_final: 0.8792 (p) REVERT: K 110 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7578 (mttp) REVERT: L 32 ASP cc_start: 0.7624 (m-30) cc_final: 0.7345 (m-30) REVERT: L 56 ASP cc_start: 0.7947 (p0) cc_final: 0.7571 (p0) outliers start: 47 outliers final: 24 residues processed: 424 average time/residue: 0.7335 time to fit residues: 365.0941 Evaluate side-chains 395 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 364 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 GLU Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain K residue 81 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN K 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.127501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084042 restraints weight = 49013.960| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.54 r_work: 0.3028 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32722 Z= 0.139 Angle : 0.628 21.526 44520 Z= 0.304 Chirality : 0.043 0.262 5009 Planarity : 0.004 0.045 5469 Dihedral : 15.234 178.204 5147 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.90 % Allowed : 26.94 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.30 (0.14), residues: 3717 helix: 1.37 (0.15), residues: 1305 sheet: -1.48 (0.21), residues: 551 loop : -0.91 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.015 0.001 TYR A1177 PHE 0.020 0.001 PHE A 361 TRP 0.015 0.001 TRP C 49 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (32693) covalent geometry : angle 0.56995 / 0.30 (44493) hydrogen bonds : bond 0.04061 / 2.73 ( 1347) hydrogen bonds : angle 5.14452 / 3.69 ( 3726) metal coordination : bond 0.01648 / 1.05 ( 29) metal coordination : angle 10.68194 / 8.19 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 406 time to evaluate : 1.241 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 66 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8103 (mp0) REVERT: A 119 VAL cc_start: 0.8359 (p) cc_final: 0.8023 (m) REVERT: A 266 MET cc_start: 0.4363 (pp-130) cc_final: 0.3784 (pp-130) REVERT: A 319 ASP cc_start: 0.8217 (t0) cc_final: 0.7868 (t0) REVERT: A 426 ARG cc_start: 0.8448 (tpp80) cc_final: 0.7941 (ttm-80) REVERT: A 734 ARG cc_start: 0.7314 (mpt-90) cc_final: 0.6900 (mpp-170) REVERT: A 762 GLU cc_start: 0.8799 (pm20) cc_final: 0.8500 (pm20) REVERT: A 861 GLN cc_start: 0.8866 (mt0) cc_final: 0.8625 (mt0) REVERT: A 1189 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7709 (p0) REVERT: A 1212 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7243 (mt) REVERT: A 1215 GLU cc_start: 0.8251 (pp20) cc_final: 0.7920 (pp20) REVERT: A 1303 GLN cc_start: 0.8451 (mp10) cc_final: 0.8053 (mp10) REVERT: A 1331 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7997 (pt) REVERT: A 1386 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8431 (mp) REVERT: A 1441 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 36 GLU cc_start: 0.8997 (tp30) cc_final: 0.8616 (tp30) REVERT: B 53 MET cc_start: 0.8428 (mpt) cc_final: 0.8183 (mpt) REVERT: B 233 SER cc_start: 0.8497 (m) cc_final: 0.8074 (p) REVERT: B 298 MET cc_start: 0.8950 (mpp) cc_final: 0.8409 (mpp) REVERT: B 344 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 407 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7694 (mtt) REVERT: B 438 ARG cc_start: 0.7671 (pmt170) cc_final: 0.7408 (ppt-90) REVERT: B 649 ASN cc_start: 0.8932 (t0) cc_final: 0.8541 (t160) REVERT: B 900 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: B 1026 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8398 (mt-10) REVERT: B 1080 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8579 (mtt180) REVERT: B 1140 CYS cc_start: 0.8679 (m) cc_final: 0.8395 (p) REVERT: B 1171 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8397 (mmm) REVERT: E 9 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8031 (mtm-85) REVERT: E 73 PHE cc_start: 0.8624 (m-80) cc_final: 0.8343 (m-10) REVERT: E 97 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: F 86 GLU cc_start: 0.8016 (mp0) cc_final: 0.7326 (mp0) REVERT: F 107 ARG cc_start: 0.8887 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: G 1 MET cc_start: 0.8006 (mpp) cc_final: 0.7628 (mmm) REVERT: H 37 MET cc_start: 0.8147 (mtp) cc_final: 0.7880 (mtp) REVERT: H 47 ILE cc_start: 0.8993 (tt) cc_final: 0.8790 (tt) REVERT: H 136 GLU cc_start: 0.8295 (pt0) cc_final: 0.7765 (pm20) REVERT: I 18 GLN cc_start: 0.8780 (mt0) cc_final: 0.8514 (mt0) REVERT: I 33 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7339 (ttm-80) REVERT: J 30 THR cc_start: 0.9230 (m) cc_final: 0.8928 (p) REVERT: J 36 ASP cc_start: 0.9007 (m-30) cc_final: 0.8729 (m-30) REVERT: K 17 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8436 (ptpp) REVERT: K 24 ASP cc_start: 0.8049 (t0) cc_final: 0.7634 (t0) REVERT: K 68 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8278 (mt-10) REVERT: L 16 ILE cc_start: 0.8660 (mm) cc_final: 0.8110 (tp) REVERT: L 32 ASP cc_start: 0.7743 (m-30) cc_final: 0.7347 (m-30) REVERT: L 35 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8097 (mtp-110) REVERT: L 56 ASP cc_start: 0.8133 (p0) cc_final: 0.7923 (p0) outliers start: 164 outliers final: 67 residues processed: 527 average time/residue: 0.6415 time to fit residues: 404.3847 Evaluate side-chains 460 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 382 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1331 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [147, 13, 136, 273, 350, 113, 175, 182, 83, 176, 56] chunk 147 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 350 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS B 420 GLN C 217 GLN C 260 GLN D 34 ASN I 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079900 restraints weight = 49117.842| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.51 r_work: 0.2961 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 32722 Z= 0.335 Angle : 0.676 18.895 44520 Z= 0.340 Chirality : 0.047 0.260 5009 Planarity : 0.005 0.045 5469 Dihedral : 15.195 179.301 5121 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 6.39 % Allowed : 26.14 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -0.52 (0.14), residues: 3717 helix: 1.08 (0.15), residues: 1309 sheet: -1.53 (0.21), residues: 543 loop : -0.98 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 16 TYR 0.019 0.002 TYR E 182 PHE 0.022 0.002 PHE A 112 TRP 0.014 0.002 TRP C 49 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.33 (32693) covalent geometry : angle 0.64999 / 0.34 (44493) hydrogen bonds : bond 0.04393 / 2.93 ( 1347) hydrogen bonds : angle 5.10738 / 3.66 ( 3726) metal coordination : bond 0.02005 / 1.27 ( 29) metal coordination : angle 7.50019 / 5.58 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 381 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8172 (mp0) REVERT: A 266 MET cc_start: 0.4282 (pp-130) cc_final: 0.3730 (pp-130) REVERT: A 319 ASP cc_start: 0.8267 (t0) cc_final: 0.7863 (t0) REVERT: A 382 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8009 (ttm110) REVERT: A 426 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8090 (ttm-80) REVERT: A 734 ARG cc_start: 0.7328 (mpt-90) cc_final: 0.6984 (mtm180) REVERT: A 861 GLN cc_start: 0.8886 (mt0) cc_final: 0.8615 (mt0) REVERT: A 940 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8123 (mptt) REVERT: A 1030 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7834 (t) REVERT: A 1215 GLU cc_start: 0.8194 (pp20) cc_final: 0.7852 (pp20) REVERT: A 1303 GLN cc_start: 0.8456 (mp10) cc_final: 0.8053 (mp10) REVERT: A 1331 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7929 (pt) REVERT: A 1350 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7000 (tmtt) REVERT: A 1386 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 1441 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 36 GLU cc_start: 0.8994 (tp30) cc_final: 0.8674 (tp30) REVERT: B 49 GLU cc_start: 0.8198 (tp30) cc_final: 0.7819 (tp30) REVERT: B 53 MET cc_start: 0.8500 (mpt) cc_final: 0.8196 (mpt) REVERT: B 233 SER cc_start: 0.8529 (m) cc_final: 0.8099 (p) REVERT: B 344 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: B 407 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7617 (mtt) REVERT: B 420 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6091 (tp-100) REVERT: B 438 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7444 (ppt-90) REVERT: B 497 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7459 (pttp) REVERT: B 634 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8330 (mp) REVERT: B 649 ASN cc_start: 0.8987 (t0) cc_final: 0.8571 (t160) REVERT: B 900 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: B 1026 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 1028 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8967 (mp) REVERT: B 1080 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8568 (mtt180) REVERT: B 1109 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: B 1140 CYS cc_start: 0.8671 (m) cc_final: 0.8238 (p) REVERT: E 9 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8082 (mtm-85) REVERT: E 97 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: E 100 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (t) REVERT: F 80 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7464 (mmm) REVERT: F 84 GLU cc_start: 0.8410 (pm20) cc_final: 0.8065 (pm20) REVERT: F 86 GLU cc_start: 0.7961 (mp0) cc_final: 0.6950 (mp0) REVERT: G 1 MET cc_start: 0.7976 (mpp) cc_final: 0.7588 (mmm) REVERT: H 37 MET cc_start: 0.8294 (mtp) cc_final: 0.8092 (mtp) REVERT: H 84 ARG cc_start: 0.8499 (pmt170) cc_final: 0.7742 (pmt-80) REVERT: H 136 GLU cc_start: 0.8244 (pt0) cc_final: 0.7728 (pm20) REVERT: I 18 GLN cc_start: 0.8724 (mt0) cc_final: 0.8448 (mt0) REVERT: I 69 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (mm) REVERT: J 30 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8885 (p) REVERT: K 18 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7822 (tptt) REVERT: K 24 ASP cc_start: 0.8063 (t0) cc_final: 0.7758 (t0) REVERT: K 38 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8553 (mm-30) REVERT: K 68 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: L 28 ILE cc_start: 0.9156 (mm) cc_final: 0.8907 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7792 (m-30) cc_final: 0.7473 (m-30) outliers start: 214 outliers final: 104 residues processed: 544 average time/residue: 0.6182 time to fit residues: 405.4946 Evaluate side-chains 493 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 367 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1331 LEU Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [184, 33, 305, 363, 248, 320, 119, 195, 118, 283, 151] chunk 184 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 283 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS A 590 GLN B 817 GLN B1094 GLN C 260 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083338 restraints weight = 48672.002| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.54 r_work: 0.3017 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32722 Z= 0.142 Angle : 0.576 15.568 44520 Z= 0.293 Chirality : 0.043 0.270 5009 Planarity : 0.004 0.043 5469 Dihedral : 15.167 179.885 5117 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.14 % Allowed : 27.63 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3717 helix: 1.27 (0.15), residues: 1307 sheet: -1.36 (0.21), residues: 550 loop : -0.83 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.012 0.001 TYR E 182 PHE 0.022 0.001 PHE A 112 TRP 0.013 0.001 TRP C 203 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (32693) covalent geometry : angle 0.56006 / 0.29 (44493) hydrogen bonds : bond 0.03670 / 2.46 ( 1347) hydrogen bonds : angle 4.84291 / 3.47 ( 3726) metal coordination : bond 0.00792 / 0.49 ( 29) metal coordination : angle 5.57567 / 4.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 410 time to evaluate : 1.257 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 66 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8145 (mp0) REVERT: A 67 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8640 (mtp180) REVERT: A 70 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7638 (mmt90) REVERT: A 266 MET cc_start: 0.4179 (pp-130) cc_final: 0.3626 (pp-130) REVERT: A 426 ARG cc_start: 0.8473 (tpp80) cc_final: 0.8207 (ttm-80) REVERT: A 734 ARG cc_start: 0.7269 (mpt-90) cc_final: 0.6998 (mtm180) REVERT: A 861 GLN cc_start: 0.8840 (mt0) cc_final: 0.8587 (mt0) REVERT: A 1030 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 1100 THR cc_start: 0.9380 (m) cc_final: 0.8975 (p) REVERT: A 1215 GLU cc_start: 0.8206 (pp20) cc_final: 0.7859 (pp20) REVERT: A 1303 GLN cc_start: 0.8445 (mp10) cc_final: 0.8032 (mp10) REVERT: A 1331 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8002 (pt) REVERT: A 1386 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 1441 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 36 GLU cc_start: 0.8999 (tp30) cc_final: 0.8650 (tp30) REVERT: B 49 GLU cc_start: 0.8142 (tp30) cc_final: 0.7775 (tp30) REVERT: B 53 MET cc_start: 0.8494 (mpt) cc_final: 0.8212 (mpt) REVERT: B 233 SER cc_start: 0.8498 (m) cc_final: 0.8040 (p) REVERT: B 298 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8361 (mpp) REVERT: B 344 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 407 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: B 438 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7253 (ppt-90) REVERT: B 649 ASN cc_start: 0.8941 (t0) cc_final: 0.8533 (t0) REVERT: B 897 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6304 (mpp-170) REVERT: B 900 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: B 1026 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 1080 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8516 (mtt180) REVERT: B 1109 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: B 1140 CYS cc_start: 0.8729 (m) cc_final: 0.8321 (p) REVERT: E 9 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8076 (mtm-85) REVERT: E 97 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: F 80 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7379 (mmm) REVERT: F 86 GLU cc_start: 0.7966 (mp0) cc_final: 0.7282 (mp0) REVERT: F 107 ARG cc_start: 0.8933 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: F 117 ASP cc_start: 0.9270 (m-30) cc_final: 0.8986 (m-30) REVERT: G 1 MET cc_start: 0.8022 (mpp) cc_final: 0.7580 (mmm) REVERT: H 84 ARG cc_start: 0.8401 (pmt170) cc_final: 0.7581 (pmt-80) REVERT: H 103 GLU cc_start: 0.8553 (pm20) cc_final: 0.8300 (pm20) REVERT: H 136 GLU cc_start: 0.8280 (pt0) cc_final: 0.7741 (pm20) REVERT: I 69 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8436 (mt) REVERT: I 74 GLN cc_start: 0.8510 (mt0) cc_final: 0.8218 (pt0) REVERT: I 93 GLU cc_start: 0.9040 (tt0) cc_final: 0.8691 (tp30) REVERT: J 30 THR cc_start: 0.9182 (m) cc_final: 0.8838 (p) REVERT: J 36 ASP cc_start: 0.9011 (m-30) cc_final: 0.8735 (m-30) REVERT: K 24 ASP cc_start: 0.8066 (t0) cc_final: 0.7665 (t0) REVERT: K 68 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8323 (mt-10) REVERT: L 28 ILE cc_start: 0.9181 (mm) cc_final: 0.8976 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7808 (m-30) cc_final: 0.7448 (m-30) outliers start: 172 outliers final: 76 residues processed: 539 average time/residue: 0.6281 time to fit residues: 405.9023 Evaluate side-chains 473 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 380 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1331 LEU Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1080 ARG Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [287, 33, 177, 9, 182, 313, 44, 321, 360, 2, 24] chunk 287 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 182 optimal weight: 0.0970 chunk 313 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 321 optimal weight: 0.6980 chunk 360 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS B 725 GLN C 260 GLN I 41 ASN I 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084476 restraints weight = 49149.381| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.56 r_work: 0.3031 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32722 Z= 0.120 Angle : 0.562 13.461 44520 Z= 0.287 Chirality : 0.043 0.259 5009 Planarity : 0.004 0.043 5469 Dihedral : 15.115 178.729 5115 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.99 % Allowed : 28.05 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -0.12 (0.14), residues: 3717 helix: 1.45 (0.15), residues: 1301 sheet: -1.19 (0.22), residues: 532 loop : -0.80 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.022 0.001 TYR A1383 PHE 0.014 0.001 PHE A 361 TRP 0.012 0.001 TRP C 203 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (32693) covalent geometry : angle 0.55089 / 0.29 (44493) hydrogen bonds : bond 0.03433 / 2.29 ( 1347) hydrogen bonds : angle 4.68934 / 3.36 ( 3726) metal coordination : bond 0.00799 / 0.51 ( 29) metal coordination : angle 4.62785 / 3.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 417 time to evaluate : 1.177 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 66 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8153 (mp0) REVERT: A 67 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8618 (mtp180) REVERT: A 70 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7738 (mmt90) REVERT: A 266 MET cc_start: 0.4105 (OUTLIER) cc_final: 0.3576 (pp-130) REVERT: A 426 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7925 (ttm-80) REVERT: A 734 ARG cc_start: 0.7274 (mpt-90) cc_final: 0.7023 (mtm180) REVERT: A 762 GLU cc_start: 0.8790 (pm20) cc_final: 0.8551 (pm20) REVERT: A 769 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: A 861 GLN cc_start: 0.8850 (mt0) cc_final: 0.8637 (mt0) REVERT: A 1030 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.7823 (t) REVERT: A 1215 GLU cc_start: 0.8208 (pp20) cc_final: 0.7837 (pp20) REVERT: A 1292 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8349 (ptp) REVERT: A 1303 GLN cc_start: 0.8489 (mp10) cc_final: 0.8078 (mp10) REVERT: A 1382 LEU cc_start: 0.8682 (mp) cc_final: 0.8390 (tp) REVERT: A 1386 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 1441 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 36 GLU cc_start: 0.9021 (tp30) cc_final: 0.8698 (tp30) REVERT: B 49 GLU cc_start: 0.8166 (tp30) cc_final: 0.7808 (tp30) REVERT: B 53 MET cc_start: 0.8524 (mpt) cc_final: 0.8241 (mpt) REVERT: B 60 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8168 (pp20) REVERT: B 233 SER cc_start: 0.8477 (m) cc_final: 0.8013 (p) REVERT: B 344 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: B 347 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: B 407 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7686 (mtt) REVERT: B 649 ASN cc_start: 0.8922 (t0) cc_final: 0.8488 (t0) REVERT: B 675 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8907 (mt) REVERT: B 897 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6239 (mpp-170) REVERT: B 900 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: B 1026 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 1080 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8545 (mtt180) REVERT: B 1109 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: B 1140 CYS cc_start: 0.8788 (m) cc_final: 0.8346 (p) REVERT: E 9 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8108 (mtm-85) REVERT: E 97 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: E 108 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: E 121 MET cc_start: 0.6903 (tpp) cc_final: 0.6651 (tpp) REVERT: E 153 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7471 (tttt) REVERT: F 80 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7427 (mmm) REVERT: F 86 GLU cc_start: 0.7941 (mp0) cc_final: 0.7285 (mp0) REVERT: G 1 MET cc_start: 0.8043 (mpp) cc_final: 0.7655 (mmm) REVERT: H 20 LYS cc_start: 0.9022 (tttp) cc_final: 0.8607 (tptt) REVERT: H 84 ARG cc_start: 0.8412 (pmt170) cc_final: 0.7603 (pmt-80) REVERT: H 103 GLU cc_start: 0.8532 (pm20) cc_final: 0.8268 (pm20) REVERT: H 136 GLU cc_start: 0.8337 (pt0) cc_final: 0.7795 (pm20) REVERT: I 69 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (mt) REVERT: I 93 GLU cc_start: 0.9052 (tt0) cc_final: 0.8576 (tm-30) REVERT: J 30 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8830 (p) REVERT: J 36 ASP cc_start: 0.9036 (m-30) cc_final: 0.8756 (m-30) REVERT: K 24 ASP cc_start: 0.8080 (t0) cc_final: 0.7661 (t0) REVERT: K 38 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8593 (mm-30) REVERT: L 28 ILE cc_start: 0.9252 (mm) cc_final: 0.9010 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7841 (m-30) cc_final: 0.7499 (m-30) REVERT: L 35 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8114 (mtp-110) outliers start: 167 outliers final: 82 residues processed: 536 average time/residue: 0.6462 time to fit residues: 414.0235 Evaluate side-chains 490 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 387 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1292 MET Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [56, 125, 312, 43, 314, 127, 248, 81, 144, 207, 356] chunk 56 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 314 optimal weight: 30.0000 chunk 127 optimal weight: 0.9980 chunk 248 optimal weight: 0.1980 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 356 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1094 GLN C 260 GLN I 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.127923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084268 restraints weight = 49148.824| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.56 r_work: 0.3031 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32722 Z= 0.136 Angle : 0.572 16.135 44520 Z= 0.289 Chirality : 0.043 0.258 5009 Planarity : 0.004 0.044 5469 Dihedral : 15.092 178.977 5115 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.17 % Allowed : 28.29 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 3717 helix: 1.46 (0.15), residues: 1302 sheet: -1.12 (0.22), residues: 532 loop : -0.76 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.013 0.001 TYR I 54 PHE 0.018 0.001 PHE A 112 TRP 0.011 0.001 TRP C 49 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (32693) covalent geometry : angle 0.56113 / 0.29 (44493) hydrogen bonds : bond 0.03422 / 2.28 ( 1347) hydrogen bonds : angle 4.62760 / 3.32 ( 3726) metal coordination : bond 0.00757 / 0.44 ( 29) metal coordination : angle 4.53422 / 3.43 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 394 time to evaluate : 1.213 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 66 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8168 (mp0) REVERT: A 67 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8667 (mtp180) REVERT: A 70 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7707 (mmt90) REVERT: A 119 VAL cc_start: 0.8353 (p) cc_final: 0.8106 (m) REVERT: A 266 MET cc_start: 0.4124 (OUTLIER) cc_final: 0.3591 (pp-130) REVERT: A 334 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7665 (mtp85) REVERT: A 426 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7914 (ttm-80) REVERT: A 734 ARG cc_start: 0.7312 (mpt-90) cc_final: 0.7066 (mtm180) REVERT: A 762 GLU cc_start: 0.8766 (pm20) cc_final: 0.8488 (pm20) REVERT: A 769 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (mtm) REVERT: A 861 GLN cc_start: 0.8843 (mt0) cc_final: 0.8611 (mt0) REVERT: A 1030 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 1167 ARG cc_start: 0.8878 (tpt90) cc_final: 0.8409 (tpm-80) REVERT: A 1215 GLU cc_start: 0.8202 (pp20) cc_final: 0.7835 (pp20) REVERT: A 1303 GLN cc_start: 0.8507 (mp10) cc_final: 0.8100 (mp10) REVERT: A 1382 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8349 (tp) REVERT: A 1386 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 1441 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 36 GLU cc_start: 0.9023 (tp30) cc_final: 0.8714 (tp30) REVERT: B 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7836 (tp30) REVERT: B 53 MET cc_start: 0.8528 (mpt) cc_final: 0.8308 (mpt) REVERT: B 60 GLU cc_start: 0.8390 (pp20) cc_final: 0.8184 (pp20) REVERT: B 233 SER cc_start: 0.8485 (m) cc_final: 0.8021 (p) REVERT: B 298 MET cc_start: 0.8931 (mpp) cc_final: 0.8451 (mpp) REVERT: B 344 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: B 347 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7844 (ttm) REVERT: B 407 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7665 (mtt) REVERT: B 649 ASN cc_start: 0.8893 (t0) cc_final: 0.8475 (t0) REVERT: B 675 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8894 (mt) REVERT: B 900 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: B 1026 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 1028 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9006 (mp) REVERT: B 1080 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8547 (mtt180) REVERT: B 1109 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8576 (mt-10) REVERT: B 1140 CYS cc_start: 0.8838 (m) cc_final: 0.8430 (p) REVERT: E 9 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (mtm-85) REVERT: E 62 VAL cc_start: 0.8744 (m) cc_final: 0.8507 (m) REVERT: E 73 PHE cc_start: 0.8873 (m-80) cc_final: 0.8665 (m-80) REVERT: E 108 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: E 121 MET cc_start: 0.7032 (tpp) cc_final: 0.6641 (tpp) REVERT: E 153 LYS cc_start: 0.8035 (mmtp) cc_final: 0.7457 (tttt) REVERT: F 80 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7438 (mmm) REVERT: F 86 GLU cc_start: 0.7969 (mp0) cc_final: 0.7330 (mp0) REVERT: G 1 MET cc_start: 0.8024 (mpp) cc_final: 0.7644 (mmm) REVERT: H 20 LYS cc_start: 0.9011 (tttp) cc_final: 0.8614 (tptt) REVERT: H 84 ARG cc_start: 0.8384 (pmt170) cc_final: 0.7613 (pmt-80) REVERT: H 103 GLU cc_start: 0.8527 (pm20) cc_final: 0.8271 (pm20) REVERT: H 136 GLU cc_start: 0.8326 (pt0) cc_final: 0.7795 (pm20) REVERT: I 69 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8453 (mt) REVERT: I 93 GLU cc_start: 0.9044 (tt0) cc_final: 0.8568 (tm-30) REVERT: J 30 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8771 (p) REVERT: J 36 ASP cc_start: 0.9035 (m-30) cc_final: 0.8728 (m-30) REVERT: K 18 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7685 (tptt) REVERT: K 24 ASP cc_start: 0.8081 (t0) cc_final: 0.7671 (t0) REVERT: K 38 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8431 (mm-30) REVERT: L 28 ILE cc_start: 0.9270 (mm) cc_final: 0.9022 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7884 (m-30) cc_final: 0.7527 (m-30) REVERT: L 35 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8118 (mtp-110) outliers start: 173 outliers final: 91 residues processed: 525 average time/residue: 0.6254 time to fit residues: 394.4795 Evaluate side-chains 494 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 381 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1080 ARG Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [3, 248, 225, 364, 0, 245, 288, 350, 212, 267, 260] chunk 3 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 364 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 260 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN I 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083112 restraints weight = 49319.022| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.54 r_work: 0.3014 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32722 Z= 0.185 Angle : 0.591 12.789 44520 Z= 0.299 Chirality : 0.044 0.262 5009 Planarity : 0.004 0.044 5469 Dihedral : 15.104 179.928 5115 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.66 % Allowed : 28.94 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -0.09 (0.14), residues: 3717 helix: 1.45 (0.15), residues: 1303 sheet: -1.18 (0.21), residues: 547 loop : -0.76 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 16 TYR 0.022 0.001 TYR A1383 PHE 0.014 0.001 PHE A 548 TRP 0.012 0.001 TRP C 49 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (32693) covalent geometry : angle 0.58096 / 0.30 (44493) hydrogen bonds : bond 0.03544 / 2.37 ( 1347) hydrogen bonds : angle 4.63445 / 3.32 ( 3726) metal coordination : bond 0.00826 / 0.48 ( 29) metal coordination : angle 4.39612 / 3.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 385 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8161 (mp0) REVERT: A 67 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8679 (mtp180) REVERT: A 70 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7676 (mmt90) REVERT: A 119 VAL cc_start: 0.8361 (p) cc_final: 0.8086 (m) REVERT: A 266 MET cc_start: 0.4183 (OUTLIER) cc_final: 0.3632 (pp-130) REVERT: A 334 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7683 (mtp85) REVERT: A 382 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8058 (ttm110) REVERT: A 426 ARG cc_start: 0.8465 (tpp80) cc_final: 0.8185 (ttm-80) REVERT: A 493 ASN cc_start: 0.9233 (t0) cc_final: 0.8899 (t0) REVERT: A 734 ARG cc_start: 0.7296 (mpt-90) cc_final: 0.7084 (mtm180) REVERT: A 861 GLN cc_start: 0.8830 (mt0) cc_final: 0.8610 (mt0) REVERT: A 1030 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7826 (t) REVERT: A 1215 GLU cc_start: 0.8223 (pp20) cc_final: 0.7837 (pp20) REVERT: A 1303 GLN cc_start: 0.8495 (mp10) cc_final: 0.8092 (mp10) REVERT: A 1386 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 1441 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: B 36 GLU cc_start: 0.9010 (tp30) cc_final: 0.8695 (tp30) REVERT: B 49 GLU cc_start: 0.8145 (tp30) cc_final: 0.7793 (tp30) REVERT: B 53 MET cc_start: 0.8486 (mpt) cc_final: 0.8236 (mpt) REVERT: B 109 MET cc_start: 0.8396 (mmm) cc_final: 0.8086 (mmt) REVERT: B 233 SER cc_start: 0.8476 (m) cc_final: 0.7859 (p) REVERT: B 298 MET cc_start: 0.8916 (mpp) cc_final: 0.8427 (mpp) REVERT: B 344 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: B 347 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7863 (ttm) REVERT: B 407 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: B 649 ASN cc_start: 0.8922 (t0) cc_final: 0.8477 (t0) REVERT: B 675 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8848 (mt) REVERT: B 900 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: B 1026 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 1028 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.8994 (mp) REVERT: B 1080 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8501 (mtt180) REVERT: B 1109 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: B 1140 CYS cc_start: 0.8717 (m) cc_final: 0.8170 (p) REVERT: E 9 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8094 (mtm-85) REVERT: E 62 VAL cc_start: 0.8682 (m) cc_final: 0.8428 (m) REVERT: E 73 PHE cc_start: 0.8929 (m-80) cc_final: 0.8599 (m-80) REVERT: E 108 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: E 121 MET cc_start: 0.7075 (tpp) cc_final: 0.6816 (tpp) REVERT: E 153 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7453 (tttt) REVERT: F 80 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.7403 (mmm) REVERT: F 86 GLU cc_start: 0.7944 (mp0) cc_final: 0.7282 (mp0) REVERT: G 1 MET cc_start: 0.8050 (mpp) cc_final: 0.7600 (mmm) REVERT: H 45 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8304 (mp) REVERT: H 84 ARG cc_start: 0.8355 (pmt170) cc_final: 0.7570 (pmt-80) REVERT: H 103 GLU cc_start: 0.8508 (pm20) cc_final: 0.8247 (pm20) REVERT: H 136 GLU cc_start: 0.8344 (pt0) cc_final: 0.7812 (pm20) REVERT: I 69 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (mt) REVERT: I 93 GLU cc_start: 0.9021 (tt0) cc_final: 0.8599 (tp30) REVERT: J 30 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8719 (p) REVERT: J 36 ASP cc_start: 0.9018 (m-30) cc_final: 0.8707 (m-30) REVERT: K 18 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7836 (tptt) REVERT: K 24 ASP cc_start: 0.8061 (t0) cc_final: 0.7714 (t0) REVERT: K 38 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8509 (mm-30) REVERT: K 68 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: L 16 ILE cc_start: 0.8645 (mm) cc_final: 0.8102 (tp) REVERT: L 28 ILE cc_start: 0.9259 (mm) cc_final: 0.9013 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7843 (m-30) cc_final: 0.7499 (m-30) REVERT: L 35 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8116 (mtp-110) outliers start: 156 outliers final: 94 residues processed: 499 average time/residue: 0.6371 time to fit residues: 380.5498 Evaluate side-chains 486 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 369 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1080 ARG Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [313, 272, 152, 232, 2, 171, 77, 115, 97, 183, 168] chunk 313 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 171 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 904 GLN B 525 ASN C 260 GLN I 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.128319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084731 restraints weight = 49309.621| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.57 r_work: 0.3040 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32722 Z= 0.127 Angle : 0.571 11.828 44520 Z= 0.290 Chirality : 0.043 0.262 5009 Planarity : 0.004 0.045 5469 Dihedral : 15.082 179.275 5115 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.27 % Allowed : 29.54 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.01 (0.14), residues: 3717 helix: 1.49 (0.15), residues: 1309 sheet: -1.03 (0.22), residues: 553 loop : -0.71 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 16 TYR 0.012 0.001 TYR B 388 PHE 0.020 0.001 PHE A 112 TRP 0.011 0.001 TRP C 49 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (32693) covalent geometry : angle 0.56352 / 0.29 (44493) hydrogen bonds : bond 0.03335 / 2.23 ( 1347) hydrogen bonds : angle 4.55487 / 3.26 ( 3726) metal coordination : bond 0.00566 / 0.35 ( 29) metal coordination : angle 3.87397 / 3.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 398 time to evaluate : 1.205 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 66 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8115 (mp0) REVERT: A 67 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8634 (mtp180) REVERT: A 70 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7695 (mmt90) REVERT: A 119 VAL cc_start: 0.8332 (p) cc_final: 0.8073 (m) REVERT: A 266 MET cc_start: 0.4091 (OUTLIER) cc_final: 0.3568 (pp-130) REVERT: A 334 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7695 (mtp85) REVERT: A 426 ARG cc_start: 0.8416 (tpp80) cc_final: 0.7955 (ttm-80) REVERT: A 493 ASN cc_start: 0.9201 (t0) cc_final: 0.8863 (t0) REVERT: A 556 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7836 (mm-30) REVERT: A 734 ARG cc_start: 0.7349 (mpt-90) cc_final: 0.7084 (mtm180) REVERT: A 762 GLU cc_start: 0.8752 (pm20) cc_final: 0.8486 (pm20) REVERT: A 769 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: A 861 GLN cc_start: 0.8797 (mt0) cc_final: 0.8560 (mt0) REVERT: A 1030 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7816 (t) REVERT: A 1215 GLU cc_start: 0.8236 (pp20) cc_final: 0.7888 (pp20) REVERT: A 1228 MET cc_start: 0.8779 (mpm) cc_final: 0.8208 (tpp) REVERT: A 1294 THR cc_start: 0.8699 (t) cc_final: 0.8475 (p) REVERT: A 1303 GLN cc_start: 0.8496 (mp10) cc_final: 0.8096 (mp10) REVERT: A 1382 LEU cc_start: 0.8698 (mp) cc_final: 0.8334 (tp) REVERT: A 1386 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 1441 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: B 36 GLU cc_start: 0.9024 (tp30) cc_final: 0.8708 (tp30) REVERT: B 49 GLU cc_start: 0.8136 (tp30) cc_final: 0.7804 (tp30) REVERT: B 53 MET cc_start: 0.8496 (mpt) cc_final: 0.8266 (mpt) REVERT: B 60 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: B 233 SER cc_start: 0.8455 (m) cc_final: 0.7840 (p) REVERT: B 298 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8374 (mpp) REVERT: B 344 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8476 (tp40) REVERT: B 407 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7587 (mtt) REVERT: B 649 ASN cc_start: 0.8891 (t0) cc_final: 0.8455 (t0) REVERT: B 675 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8854 (mt) REVERT: B 900 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: B 1026 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 1080 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8530 (mtt180) REVERT: B 1109 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: B 1140 CYS cc_start: 0.8798 (m) cc_final: 0.8295 (p) REVERT: E 9 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8083 (mtm-85) REVERT: E 62 VAL cc_start: 0.8643 (m) cc_final: 0.8354 (m) REVERT: E 73 PHE cc_start: 0.8869 (m-80) cc_final: 0.8519 (m-80) REVERT: E 97 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: E 108 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: E 121 MET cc_start: 0.6980 (tpp) cc_final: 0.6530 (tpp) REVERT: E 129 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8047 (tm-30) REVERT: E 153 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7431 (tttt) REVERT: F 80 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7330 (mmm) REVERT: F 86 GLU cc_start: 0.7943 (mp0) cc_final: 0.7287 (mp0) REVERT: G 1 MET cc_start: 0.8046 (mpp) cc_final: 0.7632 (mmm) REVERT: H 20 LYS cc_start: 0.9021 (tttp) cc_final: 0.8604 (tptt) REVERT: H 84 ARG cc_start: 0.8348 (pmt170) cc_final: 0.7587 (pmt-80) REVERT: H 103 GLU cc_start: 0.8504 (pm20) cc_final: 0.8247 (pm20) REVERT: H 136 GLU cc_start: 0.8358 (pt0) cc_final: 0.7836 (pm20) REVERT: I 69 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8434 (mt) REVERT: I 93 GLU cc_start: 0.9024 (tt0) cc_final: 0.8546 (tm-30) REVERT: J 30 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8693 (p) REVERT: J 36 ASP cc_start: 0.9017 (m-30) cc_final: 0.8719 (m-30) REVERT: K 18 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7840 (tptt) REVERT: K 24 ASP cc_start: 0.8044 (t0) cc_final: 0.7620 (t0) REVERT: K 38 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8543 (mm-30) REVERT: L 16 ILE cc_start: 0.8639 (mm) cc_final: 0.8082 (tp) REVERT: L 28 ILE cc_start: 0.9264 (mm) cc_final: 0.9010 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7888 (m-30) cc_final: 0.7519 (m-30) REVERT: L 35 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8087 (mtp-110) outliers start: 143 outliers final: 90 residues processed: 506 average time/residue: 0.6299 time to fit residues: 381.7488 Evaluate side-chains 493 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 381 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1080 ARG Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [315, 210, 367, 132, 239, 71, 261, 207, 76, 292, 139] chunk 315 optimal weight: 0.1980 chunk 210 optimal weight: 5.9990 chunk 367 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN I 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083335 restraints weight = 48906.789| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.54 r_work: 0.3015 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32722 Z= 0.192 Angle : 0.598 12.274 44520 Z= 0.304 Chirality : 0.044 0.261 5009 Planarity : 0.004 0.047 5469 Dihedral : 15.083 179.995 5115 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.06 % Allowed : 29.87 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 3717 helix: 1.44 (0.15), residues: 1310 sheet: -1.16 (0.21), residues: 555 loop : -0.71 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1167 TYR 0.020 0.001 TYR C 186 PHE 0.022 0.001 PHE A 112 TRP 0.011 0.001 TRP C 49 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (32693) covalent geometry : angle 0.59052 / 0.30 (44493) hydrogen bonds : bond 0.03503 / 2.34 ( 1347) hydrogen bonds : angle 4.60778 / 3.30 ( 3726) metal coordination : bond 0.00773 / 0.44 ( 29) metal coordination : angle 3.83041 / 2.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 373 time to evaluate : 1.242 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 66 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8152 (mp0) REVERT: A 70 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7703 (mmt90) REVERT: A 119 VAL cc_start: 0.8361 (p) cc_final: 0.8104 (m) REVERT: A 266 MET cc_start: 0.4164 (OUTLIER) cc_final: 0.3614 (pp-130) REVERT: A 334 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7690 (mtp85) REVERT: A 426 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8171 (ttm-80) REVERT: A 467 MET cc_start: 0.9057 (mpp) cc_final: 0.8818 (mpt) REVERT: A 493 ASN cc_start: 0.9245 (t0) cc_final: 0.8942 (t0) REVERT: A 734 ARG cc_start: 0.7350 (mpt-90) cc_final: 0.7126 (mtm180) REVERT: A 762 GLU cc_start: 0.8796 (pm20) cc_final: 0.8578 (pm20) REVERT: A 769 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: A 861 GLN cc_start: 0.8848 (mt0) cc_final: 0.8631 (mt0) REVERT: A 1030 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7840 (t) REVERT: A 1215 GLU cc_start: 0.8226 (pp20) cc_final: 0.7824 (pp20) REVERT: A 1228 MET cc_start: 0.8810 (mpm) cc_final: 0.8193 (tpp) REVERT: A 1294 THR cc_start: 0.8718 (t) cc_final: 0.8479 (p) REVERT: A 1303 GLN cc_start: 0.8481 (mp10) cc_final: 0.8084 (mp10) REVERT: A 1383 TYR cc_start: 0.8487 (t80) cc_final: 0.8266 (t80) REVERT: A 1386 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 1441 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: B 36 GLU cc_start: 0.9028 (tp30) cc_final: 0.8721 (tp30) REVERT: B 49 GLU cc_start: 0.8177 (tp30) cc_final: 0.7830 (tp30) REVERT: B 53 MET cc_start: 0.8537 (mpt) cc_final: 0.8282 (mpt) REVERT: B 60 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8218 (pp20) REVERT: B 233 SER cc_start: 0.8507 (m) cc_final: 0.7892 (p) REVERT: B 298 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8410 (mpp) REVERT: B 344 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: B 407 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7629 (mtt) REVERT: B 649 ASN cc_start: 0.8891 (t0) cc_final: 0.8450 (t0) REVERT: B 900 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: B 1026 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8498 (mt-10) REVERT: B 1080 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8521 (mtt180) REVERT: B 1109 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: E 9 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8126 (mtm-85) REVERT: E 62 VAL cc_start: 0.8666 (m) cc_final: 0.8425 (m) REVERT: E 73 PHE cc_start: 0.8897 (m-80) cc_final: 0.8569 (m-80) REVERT: E 97 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: E 108 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: E 121 MET cc_start: 0.7174 (tpp) cc_final: 0.6905 (tpp) REVERT: E 129 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8088 (tm-30) REVERT: E 153 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7469 (tttt) REVERT: F 80 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7401 (mmm) REVERT: F 86 GLU cc_start: 0.7955 (mp0) cc_final: 0.7289 (mp0) REVERT: G 1 MET cc_start: 0.8048 (mpp) cc_final: 0.7628 (mmm) REVERT: H 20 LYS cc_start: 0.9056 (tttp) cc_final: 0.8639 (tptt) REVERT: H 84 ARG cc_start: 0.8369 (pmt170) cc_final: 0.7611 (pmt-80) REVERT: H 103 GLU cc_start: 0.8522 (pm20) cc_final: 0.8265 (pm20) REVERT: H 136 GLU cc_start: 0.8387 (pt0) cc_final: 0.7935 (pm20) REVERT: I 93 GLU cc_start: 0.9035 (tt0) cc_final: 0.8585 (tm-30) REVERT: J 30 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8717 (p) REVERT: J 36 ASP cc_start: 0.9009 (m-30) cc_final: 0.8696 (m-30) REVERT: K 18 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7880 (tptt) REVERT: K 24 ASP cc_start: 0.8084 (t0) cc_final: 0.7758 (t0) REVERT: K 38 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8569 (mm-30) REVERT: K 68 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8618 (mt-10) REVERT: L 16 ILE cc_start: 0.8665 (mm) cc_final: 0.8111 (tp) REVERT: L 28 ILE cc_start: 0.9285 (mm) cc_final: 0.9023 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7917 (m-30) cc_final: 0.7562 (m-30) REVERT: L 35 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8085 (mtp-110) outliers start: 136 outliers final: 94 residues processed: 479 average time/residue: 0.6579 time to fit residues: 376.8804 Evaluate side-chains 485 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 371 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1168 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1416 ARG Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1080 ARG Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [366, 96, 316, 68, 184, 67, 301, 197, 240, 76, 234] chunk 366 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 316 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN G 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084284 restraints weight = 49262.353| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.56 r_work: 0.3030 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32722 Z= 0.143 Angle : 0.589 13.369 44520 Z= 0.299 Chirality : 0.043 0.264 5009 Planarity : 0.004 0.044 5469 Dihedral : 15.062 179.659 5115 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.70 % Allowed : 30.44 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -0.00 (0.14), residues: 3717 helix: 1.47 (0.15), residues: 1314 sheet: -1.05 (0.21), residues: 564 loop : -0.70 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 16 TYR 0.021 0.001 TYR C 186 PHE 0.021 0.001 PHE A 112 TRP 0.012 0.001 TRP C 49 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (32693) covalent geometry : angle 0.58163 / 0.30 (44493) hydrogen bonds : bond 0.03364 / 2.25 ( 1347) hydrogen bonds : angle 4.56170 / 3.28 ( 3726) metal coordination : bond 0.00565 / 0.35 ( 29) metal coordination : angle 3.69514 / 2.94 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 385 time to evaluate : 1.118 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 66 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8131 (mp0) REVERT: A 119 VAL cc_start: 0.8333 (p) cc_final: 0.8086 (m) REVERT: A 266 MET cc_start: 0.4143 (OUTLIER) cc_final: 0.3598 (pp-130) REVERT: A 334 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7697 (mtp85) REVERT: A 426 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8141 (ttm-80) REVERT: A 467 MET cc_start: 0.9076 (mpp) cc_final: 0.8834 (mpt) REVERT: A 493 ASN cc_start: 0.9204 (t0) cc_final: 0.8866 (t0) REVERT: A 734 ARG cc_start: 0.7357 (mpt-90) cc_final: 0.7117 (mtm180) REVERT: A 762 GLU cc_start: 0.8770 (pm20) cc_final: 0.8499 (pm20) REVERT: A 769 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (mtm) REVERT: A 861 GLN cc_start: 0.8828 (mt0) cc_final: 0.8616 (mt0) REVERT: A 1030 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7846 (t) REVERT: A 1167 ARG cc_start: 0.8872 (tpt170) cc_final: 0.8520 (tpm-80) REVERT: A 1228 MET cc_start: 0.8784 (mpm) cc_final: 0.8189 (tpp) REVERT: A 1294 THR cc_start: 0.8723 (t) cc_final: 0.8494 (p) REVERT: A 1303 GLN cc_start: 0.8491 (mp10) cc_final: 0.8130 (mp10) REVERT: A 1382 LEU cc_start: 0.8762 (mp) cc_final: 0.8381 (tp) REVERT: A 1386 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 1441 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: B 36 GLU cc_start: 0.9036 (tp30) cc_final: 0.8723 (tp30) REVERT: B 49 GLU cc_start: 0.8159 (tp30) cc_final: 0.7822 (tp30) REVERT: B 53 MET cc_start: 0.8530 (mpt) cc_final: 0.8296 (mpt) REVERT: B 60 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: B 233 SER cc_start: 0.8505 (m) cc_final: 0.7928 (p) REVERT: B 298 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8400 (mpp) REVERT: B 344 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: B 407 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: B 649 ASN cc_start: 0.8886 (t0) cc_final: 0.8471 (t0) REVERT: B 900 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: B 1026 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8489 (mt-10) REVERT: B 1080 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8558 (mtt180) REVERT: B 1109 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (mt-10) REVERT: B 1171 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8294 (mmt) REVERT: E 9 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8115 (mtm-85) REVERT: E 62 VAL cc_start: 0.8663 (m) cc_final: 0.8420 (m) REVERT: E 73 PHE cc_start: 0.8845 (m-80) cc_final: 0.8520 (m-80) REVERT: E 97 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: E 108 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: E 121 MET cc_start: 0.7116 (tpp) cc_final: 0.6829 (tpp) REVERT: E 129 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8078 (tm-30) REVERT: E 153 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7464 (tttt) REVERT: F 80 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7339 (mmm) REVERT: F 86 GLU cc_start: 0.7962 (mp0) cc_final: 0.7296 (mp0) REVERT: G 1 MET cc_start: 0.8090 (mpp) cc_final: 0.7625 (mmm) REVERT: H 20 LYS cc_start: 0.9032 (tttp) cc_final: 0.8612 (tptt) REVERT: H 47 ILE cc_start: 0.8972 (tt) cc_final: 0.8757 (tp) REVERT: H 84 ARG cc_start: 0.8373 (pmt170) cc_final: 0.7621 (pmt-80) REVERT: H 103 GLU cc_start: 0.8513 (pm20) cc_final: 0.8259 (pm20) REVERT: H 136 GLU cc_start: 0.8387 (pt0) cc_final: 0.7888 (pm20) REVERT: I 93 GLU cc_start: 0.9029 (tt0) cc_final: 0.8551 (tm-30) REVERT: J 30 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8720 (p) REVERT: J 36 ASP cc_start: 0.9027 (m-30) cc_final: 0.8734 (m-30) REVERT: K 18 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7884 (tptt) REVERT: K 24 ASP cc_start: 0.8044 (t0) cc_final: 0.7648 (t0) REVERT: K 38 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8554 (mm-30) REVERT: L 16 ILE cc_start: 0.8678 (mm) cc_final: 0.8130 (tp) REVERT: L 28 ILE cc_start: 0.9281 (mm) cc_final: 0.9020 (OUTLIER) REVERT: L 32 ASP cc_start: 0.7916 (m-30) cc_final: 0.7560 (m-30) REVERT: L 35 ARG cc_start: 0.8380 (ttp80) cc_final: 0.7893 (mtp-110) REVERT: L 42 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.7801 (mtt-85) outliers start: 124 outliers final: 89 residues processed: 479 average time/residue: 0.6524 time to fit residues: 373.4894 Evaluate side-chains 484 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 376 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1080 ARG Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: [175, 138, 34, 33, 313, 48, 286, 38, 179, 343, 328] chunk 175 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 328 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083639 restraints weight = 48971.320| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.51 r_work: 0.3021 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32722 Z= 0.190 Angle : 0.608 13.871 44520 Z= 0.309 Chirality : 0.044 0.263 5009 Planarity : 0.004 0.044 5469 Dihedral : 15.062 179.783 5115 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.64 % Allowed : 30.50 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 3717 helix: 1.43 (0.15), residues: 1310 sheet: -1.13 (0.22), residues: 551 loop : -0.71 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 16 TYR 0.021 0.001 TYR C 186 PHE 0.022 0.001 PHE A 112 TRP 0.011 0.001 TRP C 49 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (32693) covalent geometry : angle 0.60070 / 0.31 (44493) hydrogen bonds : bond 0.03531 / 2.36 ( 1347) hydrogen bonds : angle 4.60357 / 3.31 ( 3726) metal coordination : bond 0.00710 / 0.42 ( 29) metal coordination : angle 3.87766 / 3.06 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13666.97 seconds wall clock time: 232 minutes 26.70 seconds (13946.70 seconds total)