Starting phenix.real_space_refine on Mon Aug 10 05:55:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujs_64225/08_2026/9ujs_64225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujs_64225/08_2026/9ujs_64225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujs_64225/08_2026/9ujs_64225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujs_64225/08_2026/9ujs_64225.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujs_64225/08_2026/9ujs_64225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujs_64225/08_2026/9ujs_64225.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 302 5.49 5 S 210 5.16 5 C 25648 2.51 5 N 7500 2.21 5 O 8556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42216 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1408, 11095 Classifications: {'peptide': 1408} Link IDs: {'PCIS': 3, 'PTRANS': 64, 'TRANS': 1340} Chain breaks: 5 Chain: "B" Number of atoms: 9261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9261 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 52, 'TRANS': 1108} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 3 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "N" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2903 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain breaks: 1 Chain: "T" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3065 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "b" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "c" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "d" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "e" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "f" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "g" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "h" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Time building chain proxies: 8.11, per 1000 atoms: 0.19 Number of scatterers: 42216 At special positions: 0 Unit cell: (223.66, 182.32, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 210 16.00 P 302 15.00 O 8556 8.00 N 7500 7.00 C 25648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8488 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 51 sheets defined 43.3% alpha, 15.6% beta 141 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 144 removed outlier: 3.677A pdb=" N ARG A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.621A pdb=" N MET A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.532A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.631A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.536A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.809A pdb=" N MET A 456 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.514A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.698A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.874A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.696A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 662 Proline residue: A 640 - end of helix removed outlier: 3.806A pdb=" N CYS A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.510A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 846 removed outlier: 4.162A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.523A pdb=" N ASP A 872 " --> pdb=" O TYR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.502A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 removed outlier: 3.950A pdb=" N ILE A 920 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 961 through 974 removed outlier: 3.528A pdb=" N ILE A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 3.690A pdb=" N CYS A 996 " --> pdb=" O VAL A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.530A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1057 Processing helix chain 'A' and resid 1065 through 1080 Proline residue: A1077 - end of helix removed outlier: 3.754A pdb=" N GLN A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1108 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.865A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1141 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.663A pdb=" N SER A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1208 Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 4.035A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1274 Processing helix chain 'A' and resid 1315 through 1320 Processing helix chain 'A' and resid 1334 through 1360 removed outlier: 8.448A pdb=" N ILE A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N GLU A1345 " --> pdb=" O VAL A1341 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1363 No H-bonds generated for 'chain 'A' and resid 1361 through 1363' Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.757A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A1379 " --> pdb=" O VAL A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.626A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1449 through 1456 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 51 removed outlier: 3.749A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.595A pdb=" N ILE B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.815A pdb=" N LEU B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 330 removed outlier: 3.590A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 363 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 431 removed outlier: 3.737A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 removed outlier: 3.602A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.577A pdb=" N TRP B 512 " --> pdb=" O ASN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 585 through 599 removed outlier: 4.208A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.681A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 685 removed outlier: 3.532A pdb=" N GLY B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 698 removed outlier: 4.291A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 4.197A pdb=" N GLN B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.571A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.188A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 4.175A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.800A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 removed outlier: 3.515A pdb=" N GLY B1142 " --> pdb=" O MET B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.572A pdb=" N LEU C 68 " --> pdb=" O HIS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.585A pdb=" N TRP C 170 " --> pdb=" O HIS C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.675A pdb=" N GLU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.657A pdb=" N PHE D 34 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA D 35 " --> pdb=" O PRO D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 35' Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 95 through 111 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 30 through 35 removed outlier: 3.613A pdb=" N ASP E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.595A pdb=" N MET E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.127A pdb=" N VAL E 126 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 181 through 187 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.864A pdb=" N GLN F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.844A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.622A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.606A pdb=" N ALA K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.926A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 121 through 131 Processing helix chain 'b' and resid 24 through 28 Processing helix chain 'b' and resid 30 through 42 removed outlier: 3.853A pdb=" N ILE b 34 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG b 35 " --> pdb=" O LYS b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 76 removed outlier: 4.051A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 removed outlier: 3.730A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY b 94 " --> pdb=" O LEU b 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 79 removed outlier: 3.706A pdb=" N PHE c 67 " --> pdb=" O ARG c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 114 Processing helix chain 'c' and resid 120 through 132 removed outlier: 4.173A pdb=" N ILE c 124 " --> pdb=" O MET c 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 29 removed outlier: 3.712A pdb=" N ILE d 29 " --> pdb=" O ILE d 26 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 41 Processing helix chain 'd' and resid 49 through 77 removed outlier: 3.983A pdb=" N GLU d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 95 removed outlier: 3.584A pdb=" N GLN d 93 " --> pdb=" O ALA d 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.595A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE e 78 " --> pdb=" O ILE e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 47 through 49 No H-bonds generated for 'chain 'f' and resid 47 through 49' Processing helix chain 'f' and resid 50 through 77 Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.571A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 79 Processing helix chain 'g' and resid 85 through 114 Processing helix chain 'g' and resid 120 through 131 Processing helix chain 'h' and resid 24 through 29 removed outlier: 3.743A pdb=" N ILE h 29 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 41 Processing helix chain 'h' and resid 47 through 76 removed outlier: 3.822A pdb=" N TYR h 51 " --> pdb=" O SER h 47 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU h 52 " --> pdb=" O GLY h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 7.090A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.996A pdb=" N TRP A 186 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 199 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.502A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 471 removed outlier: 4.012A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 469 through 471 removed outlier: 3.640A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B1106 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 368 removed outlier: 5.870A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.390A pdb=" N LYS A 432 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 406 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 434 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.020A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA H 60 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL H 12 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR H 14 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR H 101 " --> pdb=" O TYR H 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 591 removed outlier: 7.016A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB6, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.291A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1294 " --> pdb=" O LYS A1302 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A1331 " --> pdb=" O THR A1119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1228 removed outlier: 4.577A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A1242 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A1198 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A1152 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS I 46 " --> pdb=" O THR A1152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1445 through 1448 removed outlier: 3.956A pdb=" N ASP A1445 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG F 136 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU F 144 " --> pdb=" O ARG F 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 58 removed outlier: 6.211A pdb=" N TYR B 75 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE B 124 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 77 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER B 122 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE B 79 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU B 120 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS B 81 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N MET B 119 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS B 155 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.795A pdb=" N MET B 89 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS B 97 " --> pdb=" O MET B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 6.562A pdb=" N ALA B 205 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 214 through 218 removed outlier: 4.071A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 248 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.681A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 607 " --> pdb=" O PHE B 620 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.596A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.596A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR L 31 " --> pdb=" O PHE L 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.421A pdb=" N GLY B1042 " --> pdb=" O LYS B 805 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 821 through 825 removed outlier: 8.427A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 867 Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 6.981A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.601A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1158 Processing sheet with id=AD8, first strand: chain 'B' and resid 1161 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 removed outlier: 3.572A pdb=" N GLU B1181 " --> pdb=" O ILE B1172 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.799A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 42 through 53 removed outlier: 5.263A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 47 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 6 removed outlier: 7.114A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL G 77 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.586A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.482A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.497A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.785A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF3, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AF5, first strand: chain 'a' and resid 118 through 119 removed outlier: 4.171A pdb=" N ILE a 119 " --> pdb=" O ARG b 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'g' and resid 83 through 84 removed outlier: 7.406A pdb=" N ARG g 83 " --> pdb=" O VAL h 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 1611 hydrogen bonds defined for protein. 4533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 718 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 14.51 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12388 1.34 - 1.46: 8601 1.46 - 1.58: 21664 1.58 - 1.70: 600 1.70 - 1.82: 340 Bond restraints: 43593 Sorted by residual: bond pdb=" C3' DA T 63 " pdb=" C2' DA T 63 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DT N -89 " pdb=" C2' DT N -89 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" N ILE B 429 " pdb=" CA ILE B 429 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N ILE B 612 " pdb=" CA ILE B 612 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" C3' DA N 41 " pdb=" C2' DA N 41 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 43588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 58929 2.29 - 4.58: 1049 4.58 - 6.87: 126 6.87 - 9.17: 30 9.17 - 11.46: 6 Bond angle restraints: 60140 Sorted by residual: angle pdb=" N ILE B 429 " pdb=" CA ILE B 429 " pdb=" C ILE B 429 " ideal model delta sigma weight residual 111.90 107.40 4.50 8.10e-01 1.52e+00 3.08e+01 angle pdb=" C PRO H 81 " pdb=" N LYS H 82 " pdb=" CA LYS H 82 " ideal model delta sigma weight residual 120.49 127.71 -7.22 1.42e+00 4.96e-01 2.58e+01 angle pdb=" N ILE B 612 " pdb=" CA ILE B 612 " pdb=" C ILE B 612 " ideal model delta sigma weight residual 112.96 108.25 4.71 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N3 DT T -30 " pdb=" C4 DT T -30 " pdb=" O4 DT T -30 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N VAL a 117 " pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 112.43 108.13 4.30 9.20e-01 1.18e+00 2.18e+01 ... (remaining 60135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 23882 35.69 - 71.37: 1921 71.37 - 107.06: 70 107.06 - 142.75: 1 142.75 - 178.43: 7 Dihedral angle restraints: 25881 sinusoidal: 12767 harmonic: 13114 Sorted by residual: dihedral pdb=" CA MET a 120 " pdb=" C MET a 120 " pdb=" N PRO a 121 " pdb=" CA PRO a 121 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASP C 89 " pdb=" C ASP C 89 " pdb=" N TYR C 90 " pdb=" CA TYR C 90 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLN A 46 " pdb=" C GLN A 46 " pdb=" N ARG A 47 " pdb=" CA ARG A 47 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 25878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 6696 0.130 - 0.261: 54 0.261 - 0.391: 3 0.391 - 0.521: 1 0.521 - 0.651: 5 Chirality restraints: 6759 Sorted by residual: chirality pdb=" P DC N 5 " pdb=" OP1 DC N 5 " pdb=" OP2 DC N 5 " pdb=" O5' DC N 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DG N 4 " pdb=" OP1 DG N 4 " pdb=" OP2 DG N 4 " pdb=" O5' DG N 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" P DT N 7 " pdb=" OP1 DT N 7 " pdb=" OP2 DT N 7 " pdb=" O5' DT N 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 6756 not shown) Planarity restraints: 6706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 65 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO I 66 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO I 66 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 66 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 271 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" CG ASP B 271 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP B 271 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 271 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 610 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C ASP A 610 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP A 610 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY A 611 " 0.014 2.00e-02 2.50e+03 ... (remaining 6703 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 15852 2.90 - 3.40: 42367 3.40 - 3.90: 72992 3.90 - 4.40: 81192 4.40 - 4.90: 127105 Nonbonded interactions: 339508 Sorted by model distance: nonbonded pdb=" O LYS H 82 " pdb=" OD1 ASP H 85 " model vdw 2.399 3.040 nonbonded pdb=" O GLN A 936 " pdb=" OG SER A 939 " model vdw 2.432 3.040 nonbonded pdb=" OH TYR d 88 " pdb=" NZ LYS h 59 " model vdw 2.466 3.120 nonbonded pdb=" O THR B 737 " pdb=" OG1 THR B 737 " model vdw 2.485 3.040 nonbonded pdb=" OE2 GLU B 207 " pdb=" NZ LYS B 530 " model vdw 2.495 3.120 ... (remaining 339503 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 Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'c' and resid 59 through 134) selection = chain 'e' selection = (chain 'g' and resid 59 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 94) selection = (chain 'd' and resid 25 through 94) selection = (chain 'f' and resid 25 through 94) selection = (chain 'h' and resid 25 through 94) } 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 group one per residue 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 45.680 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43593 Z= 0.315 Angle : 0.764 11.458 60140 Z= 0.513 Chirality : 0.050 0.651 6759 Planarity : 0.004 0.069 6706 Dihedral : 21.372 178.435 17393 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 0.56 % Allowed : 22.35 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.49 (0.13), residues: 4453 helix: 0.64 (0.13), residues: 1721 sheet: -1.24 (0.21), residues: 592 loop : -0.78 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 394 TYR 0.027 0.001 TYR A1155 PHE 0.034 0.002 PHE c 104 TRP 0.038 0.002 TRP B 678 HIS 0.005 0.001 HIS h 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.31 (43593) covalent geometry : angle 0.76408 / 0.51 (60140) hydrogen bonds : bond 0.16417 / 10.95 ( 1934) hydrogen bonds : angle 6.68104 / 4.71 ( 5251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 573 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8763 (mpp) cc_final: 0.8560 (mmm) REVERT: A 466 TYR cc_start: 0.8438 (m-80) cc_final: 0.8110 (m-80) REVERT: A 723 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7888 (mm) REVERT: A 1204 MET cc_start: 0.7651 (tpp) cc_final: 0.7438 (tpt) REVERT: B 305 MET cc_start: 0.8585 (pmm) cc_final: 0.7343 (pmm) REVERT: B 337 ARG cc_start: 0.7728 (mmm160) cc_final: 0.6590 (tpt170) REVERT: B 346 LYS cc_start: 0.8521 (mttt) cc_final: 0.8205 (mttt) REVERT: B 593 MET cc_start: 0.8860 (mmt) cc_final: 0.8605 (mmt) REVERT: B 1122 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8504 (ttt90) REVERT: E 109 PHE cc_start: 0.8868 (t80) cc_final: 0.8315 (t80) REVERT: E 136 GLU cc_start: 0.8062 (tp30) cc_final: 0.7740 (tp30) REVERT: G 22 MET cc_start: 0.3875 (mmm) cc_final: 0.3309 (mmm) REVERT: H 47 PHE cc_start: 0.8611 (t80) cc_final: 0.8367 (t80) REVERT: I 85 PHE cc_start: 0.7622 (p90) cc_final: 0.7362 (p90) REVERT: J 31 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8098 (mm-30) REVERT: K 76 GLN cc_start: 0.7217 (tt0) cc_final: 0.6941 (tt0) REVERT: a 76 GLN cc_start: 0.6300 (mm110) cc_final: 0.5869 (mt0) REVERT: b 63 GLU cc_start: 0.5282 (tt0) cc_final: 0.4684 (mt-10) REVERT: b 90 LEU cc_start: 0.8452 (tt) cc_final: 0.8166 (pp) REVERT: c 120 MET cc_start: 0.5118 (ptp) cc_final: 0.4783 (pmm) REVERT: d 35 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7021 (mtp85) REVERT: e 97 GLU cc_start: 0.5224 (mm-30) cc_final: 0.4099 (tp30) REVERT: f 92 ARG cc_start: 0.6147 (mmm160) cc_final: 0.5493 (tpm170) outliers start: 22 outliers final: 11 residues processed: 584 average time/residue: 0.2435 time to fit residues: 235.4859 Evaluate side-chains 530 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 517 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 133 GLU Chi-restraints excluded: chain d residue 72 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS K 106 ASN ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.169715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117067 restraints weight = 100121.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119524 restraints weight = 51677.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119902 restraints weight = 35242.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121067 restraints weight = 25901.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.121121 restraints weight = 20775.111| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43593 Z= 0.206 Angle : 0.669 9.998 60140 Z= 0.363 Chirality : 0.046 0.428 6759 Planarity : 0.004 0.051 6706 Dihedral : 23.107 178.698 8336 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 3.48 % Allowed : 20.05 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4453 helix: 0.86 (0.12), residues: 1746 sheet: -1.18 (0.20), residues: 639 loop : -0.72 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 93 TYR 0.018 0.002 TYR B 562 PHE 0.042 0.002 PHE g 104 TRP 0.015 0.001 TRP B 678 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (43593) covalent geometry : angle 0.66863 / 0.36 (60140) hydrogen bonds : bond 0.05464 / 3.74 ( 1934) hydrogen bonds : angle 5.18229 / 3.65 ( 5251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 527 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9004 (mt) REVERT: A 331 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8404 (ptpt) REVERT: A 466 TYR cc_start: 0.8441 (m-80) cc_final: 0.8105 (m-80) REVERT: A 543 GLU cc_start: 0.7866 (tp30) cc_final: 0.7638 (mm-30) REVERT: A 610 ASP cc_start: 0.8406 (t0) cc_final: 0.8174 (t0) REVERT: A 714 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 723 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 230 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 346 LYS cc_start: 0.8459 (mttt) cc_final: 0.8203 (mttt) REVERT: B 374 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8442 (mtp) REVERT: B 500 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8268 (pptt) REVERT: B 736 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.6362 (m-70) REVERT: E 109 PHE cc_start: 0.8857 (t80) cc_final: 0.8582 (t80) REVERT: F 111 ILE cc_start: 0.4152 (OUTLIER) cc_final: 0.3534 (pt) REVERT: F 116 ASP cc_start: 0.7985 (t0) cc_final: 0.7753 (t0) REVERT: G 13 LEU cc_start: 0.7292 (mp) cc_final: 0.7072 (mp) REVERT: G 22 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3559 (mmm) REVERT: H 47 PHE cc_start: 0.8627 (t80) cc_final: 0.8404 (t80) REVERT: I 62 ILE cc_start: 0.7505 (mm) cc_final: 0.7174 (mt) REVERT: J 31 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8050 (mm-30) REVERT: K 30 CYS cc_start: 0.7847 (t) cc_final: 0.7603 (t) REVERT: K 76 GLN cc_start: 0.7624 (tt0) cc_final: 0.6883 (tt0) REVERT: L 66 MET cc_start: 0.8153 (tpp) cc_final: 0.7884 (tpp) REVERT: a 76 GLN cc_start: 0.6327 (mm110) cc_final: 0.5972 (mt0) REVERT: a 84 PHE cc_start: 0.4549 (OUTLIER) cc_final: 0.4195 (m-80) REVERT: b 63 GLU cc_start: 0.5385 (tt0) cc_final: 0.4770 (mt-10) REVERT: b 79 LYS cc_start: 0.1896 (ptpp) cc_final: 0.1595 (pttp) REVERT: c 120 MET cc_start: 0.5349 (ptp) cc_final: 0.5073 (pmm) REVERT: e 97 GLU cc_start: 0.5216 (mm-30) cc_final: 0.4243 (tp30) REVERT: f 92 ARG cc_start: 0.6108 (mmm160) cc_final: 0.5562 (tpm170) outliers start: 138 outliers final: 73 residues processed: 609 average time/residue: 0.2422 time to fit residues: 245.7115 Evaluate side-chains 569 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 486 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain c residue 101 VAL Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 92 LEU Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 368 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 458 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 400 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 258 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN d 75 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.168611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.116224 restraints weight = 99650.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119146 restraints weight = 52279.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.119863 restraints weight = 31611.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120217 restraints weight = 26681.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119896 restraints weight = 22595.256| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 43593 Z= 0.215 Angle : 0.667 10.551 60140 Z= 0.359 Chirality : 0.046 0.293 6759 Planarity : 0.005 0.075 6706 Dihedral : 23.111 178.021 8319 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 4.04 % Allowed : 20.56 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.30 (0.13), residues: 4453 helix: 0.86 (0.12), residues: 1747 sheet: -1.16 (0.20), residues: 625 loop : -0.72 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 89 TYR 0.015 0.002 TYR f 51 PHE 0.042 0.002 PHE B 325 TRP 0.009 0.001 TRP G 79 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (43593) covalent geometry : angle 0.66662 / 0.36 (60140) hydrogen bonds : bond 0.05229 / 3.59 ( 1934) hydrogen bonds : angle 4.89132 / 3.44 ( 5251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 525 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7582 (tp) REVERT: A 106 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9065 (mt) REVERT: A 331 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8476 (ptpt) REVERT: A 418 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.4024 (m-80) REVERT: A 466 TYR cc_start: 0.8529 (m-80) cc_final: 0.8132 (m-10) REVERT: A 610 ASP cc_start: 0.8450 (t0) cc_final: 0.8170 (t0) REVERT: A 635 MET cc_start: 0.8946 (tpp) cc_final: 0.8658 (tpp) REVERT: A 714 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 723 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7883 (mm) REVERT: A 1203 ARG cc_start: 0.7523 (mmm160) cc_final: 0.7167 (mmm160) REVERT: A 1226 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 1331 TYR cc_start: 0.8362 (t80) cc_final: 0.7915 (t80) REVERT: B 230 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 305 MET cc_start: 0.8436 (pmm) cc_final: 0.8186 (pmm) REVERT: B 344 TYR cc_start: 0.7979 (t80) cc_final: 0.7718 (t80) REVERT: B 346 LYS cc_start: 0.8473 (mttt) cc_final: 0.8185 (mttt) REVERT: B 500 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8331 (pptt) REVERT: B 506 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8271 (mp10) REVERT: B 519 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 617 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7708 (t80) REVERT: B 736 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6418 (m-70) REVERT: C 142 ILE cc_start: 0.9376 (mp) cc_final: 0.9109 (mm) REVERT: F 111 ILE cc_start: 0.4063 (OUTLIER) cc_final: 0.3470 (pt) REVERT: F 116 ASP cc_start: 0.8096 (t0) cc_final: 0.7693 (t0) REVERT: F 119 GLN cc_start: 0.7984 (mp10) cc_final: 0.7524 (mp10) REVERT: G 13 LEU cc_start: 0.7485 (mp) cc_final: 0.7238 (mp) REVERT: G 22 MET cc_start: 0.4220 (OUTLIER) cc_final: 0.3609 (mmm) REVERT: H 82 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7627 (mttp) REVERT: I 24 ARG cc_start: 0.6654 (tmm-80) cc_final: 0.6437 (tmm-80) REVERT: J 31 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8033 (mm-30) REVERT: a 76 GLN cc_start: 0.6322 (mm110) cc_final: 0.6021 (mt0) REVERT: a 84 PHE cc_start: 0.4480 (OUTLIER) cc_final: 0.4133 (m-80) REVERT: b 62 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4777 (tp) REVERT: b 63 GLU cc_start: 0.5444 (tt0) cc_final: 0.4823 (mt-10) REVERT: b 79 LYS cc_start: 0.1994 (ptpp) cc_final: 0.1689 (pttp) REVERT: c 120 MET cc_start: 0.5169 (ptp) cc_final: 0.4963 (pmm) REVERT: e 97 GLU cc_start: 0.5207 (mm-30) cc_final: 0.4090 (tp30) REVERT: f 36 ARG cc_start: 0.2454 (ptt90) cc_final: 0.2087 (ptt90) REVERT: f 92 ARG cc_start: 0.6196 (mmm160) cc_final: 0.5682 (tpm170) outliers start: 160 outliers final: 90 residues processed: 626 average time/residue: 0.2529 time to fit residues: 265.1657 Evaluate side-chains 584 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 478 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 617 PHE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain d residue 82 THR Chi-restraints excluded: chain e residue 96 CYS Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 275 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 428 optimal weight: 8.9990 chunk 415 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 434 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 331 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 124 GLN A 446 ASN A 511 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 932 HIS ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN a 125 GLN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.166536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113193 restraints weight = 99778.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116477 restraints weight = 50976.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116429 restraints weight = 32223.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117464 restraints weight = 25574.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117854 restraints weight = 20099.313| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 43593 Z= 0.264 Angle : 0.692 11.180 60140 Z= 0.373 Chirality : 0.047 0.296 6759 Planarity : 0.005 0.068 6706 Dihedral : 23.170 179.397 8319 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 5.23 % Allowed : 21.09 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.46 (0.12), residues: 4453 helix: 0.77 (0.12), residues: 1747 sheet: -1.27 (0.20), residues: 617 loop : -0.86 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 328 TYR 0.025 0.002 TYR B 295 PHE 0.025 0.002 PHE b 61 TRP 0.011 0.001 TRP G 79 HIS 0.006 0.001 HIS B 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (43593) covalent geometry : angle 0.69228 / 0.37 (60140) hydrogen bonds : bond 0.05452 / 3.75 ( 1934) hydrogen bonds : angle 4.88144 / 3.44 ( 5251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 506 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8318 (ttt-90) cc_final: 0.8113 (ttt-90) REVERT: A 331 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8620 (ptpt) REVERT: A 418 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.4191 (m-80) REVERT: A 466 TYR cc_start: 0.8584 (m-80) cc_final: 0.8221 (m-10) REVERT: A 610 ASP cc_start: 0.8456 (t0) cc_final: 0.8153 (t0) REVERT: A 635 MET cc_start: 0.9018 (tpp) cc_final: 0.8712 (tpp) REVERT: A 723 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 1203 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7106 (mmm160) REVERT: A 1207 LYS cc_start: 0.8195 (pttm) cc_final: 0.7610 (pttm) REVERT: A 1230 TRP cc_start: 0.8582 (p-90) cc_final: 0.8043 (p90) REVERT: A 1262 MET cc_start: 0.8446 (ptp) cc_final: 0.7726 (pmm) REVERT: A 1331 TYR cc_start: 0.8519 (t80) cc_final: 0.8078 (t80) REVERT: B 230 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7265 (mt-10) REVERT: B 344 TYR cc_start: 0.8021 (t80) cc_final: 0.7650 (t80) REVERT: B 346 LYS cc_start: 0.8517 (mttt) cc_final: 0.8291 (mttt) REVERT: B 347 ASP cc_start: 0.9098 (m-30) cc_final: 0.8774 (t0) REVERT: B 500 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8368 (pptt) REVERT: B 519 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: B 617 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 736 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6263 (m-70) REVERT: B 1102 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8083 (mttm) REVERT: C 142 ILE cc_start: 0.9360 (mp) cc_final: 0.9115 (mm) REVERT: C 153 LEU cc_start: 0.8717 (tt) cc_final: 0.8438 (tp) REVERT: F 111 ILE cc_start: 0.4508 (OUTLIER) cc_final: 0.3932 (pt) REVERT: F 119 GLN cc_start: 0.7996 (mp10) cc_final: 0.7543 (mp10) REVERT: G 13 LEU cc_start: 0.7505 (mp) cc_final: 0.7266 (mp) REVERT: G 22 MET cc_start: 0.4321 (OUTLIER) cc_final: 0.3668 (mmm) REVERT: H 82 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7645 (mttp) REVERT: H 131 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7916 (mt) REVERT: I 24 ARG cc_start: 0.6762 (tmm-80) cc_final: 0.6517 (tmm-80) REVERT: I 70 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6354 (ptp90) REVERT: J 31 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8111 (mm-30) REVERT: L 68 GLN cc_start: 0.7567 (tm130) cc_final: 0.7090 (tm-30) REVERT: a 76 GLN cc_start: 0.6326 (mm110) cc_final: 0.6112 (mt0) REVERT: a 84 PHE cc_start: 0.4661 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: b 62 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4685 (tp) REVERT: b 63 GLU cc_start: 0.5418 (tt0) cc_final: 0.4831 (mt-10) REVERT: b 79 LYS cc_start: 0.2225 (ptpp) cc_final: 0.1871 (pttp) REVERT: e 97 GLU cc_start: 0.5540 (mm-30) cc_final: 0.4214 (tp30) outliers start: 207 outliers final: 131 residues processed: 651 average time/residue: 0.2548 time to fit residues: 276.2459 Evaluate side-chains 617 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 471 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 569 LYS Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 617 PHE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1102 LYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 115 PHE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain b residue 90 LEU Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain d residue 82 THR Chi-restraints excluded: chain e residue 96 CYS Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 228 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 428 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 414 optimal weight: 20.0000 chunk 462 optimal weight: 20.0000 chunk 199 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.169329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116317 restraints weight = 99536.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119519 restraints weight = 50634.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120345 restraints weight = 29976.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.121063 restraints weight = 23164.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121045 restraints weight = 20733.532| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43593 Z= 0.141 Angle : 0.626 10.155 60140 Z= 0.336 Chirality : 0.045 0.324 6759 Planarity : 0.004 0.051 6706 Dihedral : 23.127 179.558 8317 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 3.74 % Allowed : 22.45 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % Twisted Proline : 0.52 % 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: -0.23 (0.13), residues: 4453 helix: 0.94 (0.13), residues: 1746 sheet: -1.16 (0.20), residues: 620 loop : -0.71 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 35 TYR 0.033 0.001 TYR B 295 PHE 0.022 0.001 PHE b 61 TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (43593) covalent geometry : angle 0.62557 / 0.34 (60140) hydrogen bonds : bond 0.04524 / 3.12 ( 1934) hydrogen bonds : angle 4.60964 / 3.24 ( 5251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 537 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8446 (ptpt) REVERT: A 418 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.4164 (m-80) REVERT: A 466 TYR cc_start: 0.8420 (m-80) cc_final: 0.8155 (m-10) REVERT: A 610 ASP cc_start: 0.8390 (t0) cc_final: 0.8119 (t0) REVERT: A 635 MET cc_start: 0.8933 (tpp) cc_final: 0.8517 (tpp) REVERT: A 694 ILE cc_start: 0.9322 (mt) cc_final: 0.9117 (mm) REVERT: A 723 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7898 (mm) REVERT: A 1207 LYS cc_start: 0.8203 (pttm) cc_final: 0.7505 (ptmm) REVERT: A 1262 MET cc_start: 0.8379 (ptp) cc_final: 0.7654 (pmm) REVERT: A 1369 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7975 (ptp-170) REVERT: B 230 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7222 (mt-10) REVERT: B 329 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7622 (mtt-85) REVERT: B 344 TYR cc_start: 0.8021 (t80) cc_final: 0.7657 (t80) REVERT: B 346 LYS cc_start: 0.8512 (mttt) cc_final: 0.8258 (mttt) REVERT: B 347 ASP cc_start: 0.9084 (m-30) cc_final: 0.8756 (t0) REVERT: B 456 THR cc_start: 0.8721 (p) cc_final: 0.8441 (p) REVERT: B 500 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8401 (pptt) REVERT: B 736 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6270 (m-70) REVERT: B 1122 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8557 (ttt90) REVERT: B 1133 MET cc_start: 0.8035 (mtm) cc_final: 0.7770 (mmm) REVERT: B 1163 CYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8171 (p) REVERT: C 190 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7813 (t70) REVERT: F 111 ILE cc_start: 0.4307 (OUTLIER) cc_final: 0.3751 (pt) REVERT: F 116 ASP cc_start: 0.8063 (t0) cc_final: 0.7342 (t0) REVERT: F 119 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: G 13 LEU cc_start: 0.7461 (mp) cc_final: 0.7210 (mp) REVERT: G 22 MET cc_start: 0.4401 (OUTLIER) cc_final: 0.3770 (mmm) REVERT: H 82 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7645 (mttp) REVERT: I 13 MET cc_start: 0.7218 (mmp) cc_final: 0.5961 (mtt) REVERT: I 24 ARG cc_start: 0.6846 (tmm-80) cc_final: 0.6534 (tmm-80) REVERT: I 70 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6362 (ptp90) REVERT: J 30 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: K 95 ILE cc_start: 0.9297 (tt) cc_final: 0.8855 (pt) REVERT: a 84 PHE cc_start: 0.4677 (OUTLIER) cc_final: 0.4308 (m-80) REVERT: b 62 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4542 (tp) REVERT: b 63 GLU cc_start: 0.5491 (tt0) cc_final: 0.4951 (mt-10) REVERT: c 129 ARG cc_start: 0.7450 (tpm170) cc_final: 0.7134 (tpm170) REVERT: e 97 GLU cc_start: 0.5494 (mm-30) cc_final: 0.4338 (tp30) REVERT: f 92 ARG cc_start: 0.5994 (mmm160) cc_final: 0.5474 (tpm170) outliers start: 148 outliers final: 84 residues processed: 640 average time/residue: 0.2545 time to fit residues: 271.3476 Evaluate side-chains 595 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 493 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1369 ARG Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 115 PHE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 223 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 379 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 384 optimal weight: 7.9990 chunk 471 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 375 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 172 optimal weight: 0.0010 chunk 373 optimal weight: 20.0000 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 563 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** a 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 27 GLN ** d 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.164032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110317 restraints weight = 100600.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113849 restraints weight = 51116.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113765 restraints weight = 29321.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114534 restraints weight = 25088.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114912 restraints weight = 21127.519| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 43593 Z= 0.352 Angle : 0.773 11.550 60140 Z= 0.410 Chirality : 0.049 0.307 6759 Planarity : 0.005 0.064 6706 Dihedral : 23.235 175.225 8317 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 5.13 % Allowed : 21.92 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.63 (0.12), residues: 4453 helix: 0.62 (0.12), residues: 1759 sheet: -1.39 (0.19), residues: 630 loop : -0.94 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 128 TYR 0.018 0.002 TYR B 295 PHE 0.024 0.002 PHE A1335 TRP 0.012 0.002 TRP G 79 HIS 0.008 0.002 HIS B 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.35 (43593) covalent geometry : angle 0.77265 / 0.41 (60140) hydrogen bonds : bond 0.06150 / 4.23 ( 1934) hydrogen bonds : angle 4.97252 / 3.50 ( 5251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 481 time to evaluate : 1.543 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 327 ARG cc_start: 0.8415 (ttt-90) cc_final: 0.7545 (tmt170) REVERT: A 331 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8676 (ptpt) REVERT: A 418 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.4155 (m-80) REVERT: A 454 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7374 (mtp) REVERT: A 466 TYR cc_start: 0.8614 (m-80) cc_final: 0.8318 (m-10) REVERT: A 610 ASP cc_start: 0.8428 (t0) cc_final: 0.8154 (t0) REVERT: A 723 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7972 (mm) REVERT: A 823 GLU cc_start: 0.8251 (tp30) cc_final: 0.8044 (tp30) REVERT: A 832 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8694 (m) REVERT: A 1203 ARG cc_start: 0.7565 (mmm160) cc_final: 0.7224 (mmm160) REVERT: A 1207 LYS cc_start: 0.8205 (pttm) cc_final: 0.7801 (pttm) REVERT: A 1262 MET cc_start: 0.8434 (ptp) cc_final: 0.7625 (pmm) REVERT: A 1331 TYR cc_start: 0.8553 (t80) cc_final: 0.8182 (t80) REVERT: A 1429 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 230 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7412 (mt-10) REVERT: B 305 MET cc_start: 0.8571 (pmm) cc_final: 0.7875 (pmm) REVERT: B 346 LYS cc_start: 0.8537 (mttt) cc_final: 0.8310 (mttt) REVERT: B 347 ASP cc_start: 0.9163 (m-30) cc_final: 0.8813 (t0) REVERT: B 373 TYR cc_start: 0.9209 (t80) cc_final: 0.8990 (t80) REVERT: B 444 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 500 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8444 (pptt) REVERT: B 556 MET cc_start: 0.7730 (tmm) cc_final: 0.7240 (tmm) REVERT: B 617 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7942 (t80) REVERT: B 736 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.6222 (m-70) REVERT: B 875 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 1102 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8145 (mttm) REVERT: B 1122 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8570 (ttt180) REVERT: B 1163 CYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 142 ILE cc_start: 0.9335 (mp) cc_final: 0.9012 (mm) REVERT: C 190 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7857 (t70) REVERT: F 111 ILE cc_start: 0.4766 (OUTLIER) cc_final: 0.4113 (pt) REVERT: F 119 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: F 123 LYS cc_start: 0.7444 (mmtt) cc_final: 0.7242 (mmtt) REVERT: G 1 MET cc_start: 0.2480 (pmm) cc_final: 0.2222 (pmm) REVERT: G 22 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.3843 (mmm) REVERT: H 82 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7669 (mttp) REVERT: H 131 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7953 (mt) REVERT: I 70 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6521 (ptp90) REVERT: L 45 SER cc_start: 0.7168 (p) cc_final: 0.6802 (t) REVERT: a 84 PHE cc_start: 0.4829 (OUTLIER) cc_final: 0.4417 (m-80) REVERT: b 62 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.4050 (tp) REVERT: b 63 GLU cc_start: 0.5609 (tt0) cc_final: 0.5039 (mt-10) REVERT: b 79 LYS cc_start: 0.2673 (ptpp) cc_final: 0.2193 (pttp) REVERT: e 97 GLU cc_start: 0.5125 (mm-30) cc_final: 0.4094 (tp30) outliers start: 203 outliers final: 138 residues processed: 625 average time/residue: 0.2582 time to fit residues: 268.1468 Evaluate side-chains 613 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 453 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 569 LYS Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 617 PHE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1102 LYS Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 101 VAL Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain d residue 82 THR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 96 CYS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 51 TYR Chi-restraints excluded: chain g residue 80 THR Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 336 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 366 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 433 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 ASN ** h 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.167868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.114881 restraints weight = 99100.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118474 restraints weight = 49393.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119064 restraints weight = 29188.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.120321 restraints weight = 21462.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.119961 restraints weight = 19379.587| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43593 Z= 0.143 Angle : 0.650 10.725 60140 Z= 0.345 Chirality : 0.045 0.340 6759 Planarity : 0.004 0.070 6706 Dihedral : 23.210 177.083 8317 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 3.38 % Allowed : 23.48 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4453 helix: 0.84 (0.12), residues: 1757 sheet: -1.26 (0.19), residues: 625 loop : -0.78 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 129 TYR 0.018 0.001 TYR I 44 PHE 0.027 0.002 PHE h 61 TRP 0.012 0.001 TRP C 201 HIS 0.006 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (43593) covalent geometry : angle 0.64993 / 0.35 (60140) hydrogen bonds : bond 0.04541 / 3.14 ( 1934) hydrogen bonds : angle 4.59608 / 3.23 ( 5251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 512 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8285 (ttt-90) cc_final: 0.7612 (tmt170) REVERT: A 331 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8538 (ptpt) REVERT: A 418 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.4182 (m-80) REVERT: A 466 TYR cc_start: 0.8491 (m-80) cc_final: 0.8140 (m-10) REVERT: A 723 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7952 (mm) REVERT: A 1203 ARG cc_start: 0.7395 (mmm160) cc_final: 0.7086 (mmm160) REVERT: A 1230 TRP cc_start: 0.8636 (p-90) cc_final: 0.8106 (p90) REVERT: A 1262 MET cc_start: 0.8389 (ptp) cc_final: 0.7583 (pmm) REVERT: B 230 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7349 (mt-10) REVERT: B 344 TYR cc_start: 0.8013 (t80) cc_final: 0.7643 (t80) REVERT: B 346 LYS cc_start: 0.8517 (mttt) cc_final: 0.8273 (mttt) REVERT: B 347 ASP cc_start: 0.9104 (m-30) cc_final: 0.8799 (t0) REVERT: B 456 THR cc_start: 0.8710 (p) cc_final: 0.8458 (p) REVERT: B 500 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8483 (pptt) REVERT: B 556 MET cc_start: 0.7600 (tmm) cc_final: 0.7062 (tmm) REVERT: B 736 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6245 (m-70) REVERT: B 969 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7810 (ttm170) REVERT: B 1122 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8228 (ttt180) REVERT: B 1163 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8095 (p) REVERT: C 142 ILE cc_start: 0.9349 (mp) cc_final: 0.9100 (mm) REVERT: C 190 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7855 (t70) REVERT: F 111 ILE cc_start: 0.4150 (OUTLIER) cc_final: 0.3790 (pt) REVERT: F 119 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: G 13 LEU cc_start: 0.7614 (mp) cc_final: 0.7372 (mp) REVERT: G 22 MET cc_start: 0.4441 (OUTLIER) cc_final: 0.3754 (mmm) REVERT: H 82 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7636 (mttp) REVERT: I 13 MET cc_start: 0.7522 (mmp) cc_final: 0.6380 (mtt) REVERT: I 24 ARG cc_start: 0.6953 (tmm-80) cc_final: 0.6691 (tmm-80) REVERT: I 70 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6537 (ptp90) REVERT: K 95 ILE cc_start: 0.9325 (tt) cc_final: 0.8853 (pt) REVERT: L 45 SER cc_start: 0.7128 (p) cc_final: 0.6760 (t) REVERT: a 84 PHE cc_start: 0.4815 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: b 63 GLU cc_start: 0.5603 (tt0) cc_final: 0.4914 (mt-10) REVERT: b 79 LYS cc_start: 0.2501 (ptpp) cc_final: 0.2129 (pttp) REVERT: e 97 GLU cc_start: 0.5402 (mm-30) cc_final: 0.4180 (tp30) REVERT: f 37 LEU cc_start: 0.4400 (mt) cc_final: 0.3921 (mt) outliers start: 134 outliers final: 94 residues processed: 602 average time/residue: 0.2580 time to fit residues: 258.7416 Evaluate side-chains 593 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 484 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 115 PHE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 406 optimal weight: 40.0000 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 464 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 247 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 ASN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.168437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115542 restraints weight = 99828.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118977 restraints weight = 49817.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119316 restraints weight = 31234.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120342 restraints weight = 22283.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.120454 restraints weight = 19368.636| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43593 Z= 0.140 Angle : 0.638 12.269 60140 Z= 0.338 Chirality : 0.044 0.332 6759 Planarity : 0.004 0.093 6706 Dihedral : 23.114 175.495 8317 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 3.51 % Allowed : 23.99 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.22 (0.13), residues: 4453 helix: 0.92 (0.12), residues: 1755 sheet: -1.04 (0.20), residues: 622 loop : -0.72 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG d 55 TYR 0.022 0.001 TYR B 562 PHE 0.030 0.001 PHE g 78 TRP 0.011 0.001 TRP C 201 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (43593) covalent geometry : angle 0.63794 / 0.34 (60140) hydrogen bonds : bond 0.04353 / 3.01 ( 1934) hydrogen bonds : angle 4.47676 / 3.15 ( 5251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 513 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LYS cc_start: 0.8996 (mttm) cc_final: 0.8533 (tptt) REVERT: A 327 ARG cc_start: 0.8112 (ttt-90) cc_final: 0.7507 (tmt170) REVERT: A 331 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8435 (ptpt) REVERT: A 394 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8176 (mtm110) REVERT: A 418 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.4154 (m-80) REVERT: A 466 TYR cc_start: 0.8496 (m-80) cc_final: 0.8109 (m-10) REVERT: A 635 MET cc_start: 0.8442 (tpp) cc_final: 0.8160 (ttt) REVERT: A 723 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 1203 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7238 (mmm160) REVERT: A 1207 LYS cc_start: 0.8194 (pttm) cc_final: 0.7745 (pttm) REVERT: A 1230 TRP cc_start: 0.8709 (p-90) cc_final: 0.8316 (p90) REVERT: A 1262 MET cc_start: 0.8372 (ptp) cc_final: 0.7674 (pmm) REVERT: B 52 GLU cc_start: 0.8522 (tp30) cc_final: 0.8317 (tp30) REVERT: B 230 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7235 (mt-10) REVERT: B 344 TYR cc_start: 0.8029 (t80) cc_final: 0.7644 (t80) REVERT: B 346 LYS cc_start: 0.8462 (mttt) cc_final: 0.8207 (mttt) REVERT: B 347 ASP cc_start: 0.9097 (m-30) cc_final: 0.8806 (t0) REVERT: B 456 THR cc_start: 0.8674 (p) cc_final: 0.8442 (p) REVERT: B 500 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8516 (pptt) REVERT: B 736 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6284 (m-70) REVERT: B 1122 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8231 (ttt180) REVERT: B 1163 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8010 (p) REVERT: C 142 ILE cc_start: 0.9348 (mp) cc_final: 0.9086 (mm) REVERT: C 190 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7867 (t70) REVERT: F 111 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3813 (pt) REVERT: F 119 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: G 13 LEU cc_start: 0.7699 (mp) cc_final: 0.7464 (mp) REVERT: G 22 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3812 (mmm) REVERT: H 82 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7629 (mttp) REVERT: I 13 MET cc_start: 0.7527 (mmp) cc_final: 0.6568 (mtt) REVERT: I 70 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6519 (ptp90) REVERT: J 30 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: K 39 ASP cc_start: 0.8655 (p0) cc_final: 0.8347 (p0) REVERT: L 45 SER cc_start: 0.7120 (p) cc_final: 0.6750 (t) REVERT: a 84 PHE cc_start: 0.4787 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: b 62 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4709 (tp) REVERT: b 63 GLU cc_start: 0.5187 (tt0) cc_final: 0.4785 (mt-10) REVERT: b 79 LYS cc_start: 0.2451 (ptpp) cc_final: 0.2024 (pttp) REVERT: e 97 GLU cc_start: 0.5435 (mm-30) cc_final: 0.4221 (tp30) REVERT: f 37 LEU cc_start: 0.4421 (mt) cc_final: 0.4201 (mp) outliers start: 139 outliers final: 97 residues processed: 604 average time/residue: 0.2612 time to fit residues: 263.2745 Evaluate side-chains 603 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 490 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 115 PHE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 96 CYS Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 260 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 413 optimal weight: 30.0000 chunk 173 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN d 64 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.167359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114170 restraints weight = 99640.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.118059 restraints weight = 49759.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118036 restraints weight = 28706.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119159 restraints weight = 22964.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119167 restraints weight = 19747.813| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43593 Z= 0.177 Angle : 0.657 11.881 60140 Z= 0.347 Chirality : 0.045 0.324 6759 Planarity : 0.004 0.070 6706 Dihedral : 23.088 174.176 8317 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 3.48 % Allowed : 24.19 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.20 (0.13), residues: 4453 helix: 0.96 (0.12), residues: 1756 sheet: -1.00 (0.20), residues: 617 loop : -0.73 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 977 TYR 0.040 0.001 TYR E 111 PHE 0.026 0.002 PHE g 78 TRP 0.010 0.001 TRP G 79 HIS 0.009 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (43593) covalent geometry : angle 0.65703 / 0.35 (60140) hydrogen bonds : bond 0.04524 / 3.13 ( 1934) hydrogen bonds : angle 4.48607 / 3.16 ( 5251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 502 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7335 (pmt-80) REVERT: A 132 LYS cc_start: 0.9008 (mttm) cc_final: 0.8546 (tptt) REVERT: A 327 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7438 (tmt170) REVERT: A 331 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8415 (ptpt) REVERT: A 418 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.4231 (m-80) REVERT: A 466 TYR cc_start: 0.8473 (m-80) cc_final: 0.8169 (m-10) REVERT: A 543 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 570 LYS cc_start: 0.8732 (tttt) cc_final: 0.8456 (ttpp) REVERT: A 635 MET cc_start: 0.8601 (tpp) cc_final: 0.8367 (tpt) REVERT: A 723 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 1207 LYS cc_start: 0.8166 (pttm) cc_final: 0.7612 (pttm) REVERT: A 1230 TRP cc_start: 0.8688 (p-90) cc_final: 0.8291 (p90) REVERT: A 1262 MET cc_start: 0.8361 (ptp) cc_final: 0.7656 (pmm) REVERT: A 1354 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 52 GLU cc_start: 0.8488 (tp30) cc_final: 0.8285 (tp30) REVERT: B 230 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7268 (mt-10) REVERT: B 344 TYR cc_start: 0.7990 (t80) cc_final: 0.7736 (t80) REVERT: B 346 LYS cc_start: 0.8471 (mttt) cc_final: 0.8210 (mttt) REVERT: B 347 ASP cc_start: 0.9097 (m-30) cc_final: 0.8801 (t0) REVERT: B 373 TYR cc_start: 0.9173 (t80) cc_final: 0.8903 (t80) REVERT: B 456 THR cc_start: 0.8714 (p) cc_final: 0.8485 (p) REVERT: B 500 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8478 (pptt) REVERT: B 556 MET cc_start: 0.7661 (tmm) cc_final: 0.7180 (tmm) REVERT: B 736 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.6261 (m-70) REVERT: B 1122 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8324 (ttt180) REVERT: B 1163 CYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8178 (p) REVERT: C 142 ILE cc_start: 0.9339 (mp) cc_final: 0.9068 (mm) REVERT: C 190 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7862 (t70) REVERT: F 111 ILE cc_start: 0.4281 (OUTLIER) cc_final: 0.3942 (pt) REVERT: F 114 GLU cc_start: 0.6838 (pm20) cc_final: 0.6620 (pm20) REVERT: F 119 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: G 13 LEU cc_start: 0.7725 (mp) cc_final: 0.7489 (mp) REVERT: G 22 MET cc_start: 0.4576 (OUTLIER) cc_final: 0.3878 (mmm) REVERT: H 82 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7663 (mttp) REVERT: I 13 MET cc_start: 0.7554 (mmp) cc_final: 0.6641 (mtt) REVERT: I 70 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6554 (ptp90) REVERT: J 30 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: K 36 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7587 (mm-30) REVERT: L 45 SER cc_start: 0.7128 (p) cc_final: 0.6756 (t) REVERT: a 84 PHE cc_start: 0.4861 (OUTLIER) cc_final: 0.4529 (m-80) REVERT: b 44 LYS cc_start: 0.7904 (mmtm) cc_final: 0.6574 (ptmt) REVERT: b 62 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.4622 (tp) REVERT: b 63 GLU cc_start: 0.5176 (tt0) cc_final: 0.4601 (mt-10) REVERT: b 79 LYS cc_start: 0.2360 (ptpp) cc_final: 0.1932 (pttp) REVERT: d 50 ILE cc_start: 0.5029 (OUTLIER) cc_final: 0.4823 (tp) REVERT: e 97 GLU cc_start: 0.5269 (mm-30) cc_final: 0.4193 (tp30) outliers start: 138 outliers final: 106 residues processed: 598 average time/residue: 0.2579 time to fit residues: 257.7111 Evaluate side-chains 602 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 479 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 115 PHE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain d residue 64 ASN Chi-restraints excluded: chain d residue 72 TYR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 96 CYS Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 452 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 427 optimal weight: 10.0000 chunk 49 optimal weight: 0.0970 chunk 231 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.167739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114520 restraints weight = 99612.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118579 restraints weight = 48876.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.118633 restraints weight = 27962.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119675 restraints weight = 21843.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119691 restraints weight = 19836.455| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43593 Z= 0.160 Angle : 0.657 12.066 60140 Z= 0.345 Chirality : 0.045 0.330 6759 Planarity : 0.004 0.082 6706 Dihedral : 23.078 174.394 8317 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 3.31 % Allowed : 24.57 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.16 (0.13), residues: 4453 helix: 0.97 (0.12), residues: 1754 sheet: -0.93 (0.20), residues: 615 loop : -0.71 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG d 55 TYR 0.038 0.001 TYR E 111 PHE 0.022 0.002 PHE g 78 TRP 0.009 0.001 TRP G 79 HIS 0.007 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (43593) covalent geometry : angle 0.65659 / 0.35 (60140) hydrogen bonds : bond 0.04390 / 3.04 ( 1934) hydrogen bonds : angle 4.45872 / 3.14 ( 5251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 498 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7696 (tmm-80) cc_final: 0.7274 (pmt-80) REVERT: A 132 LYS cc_start: 0.8995 (mttm) cc_final: 0.8545 (tptt) REVERT: A 327 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7511 (tmt170) REVERT: A 331 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8426 (ptpt) REVERT: A 418 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.4230 (m-80) REVERT: A 466 TYR cc_start: 0.8463 (m-80) cc_final: 0.8161 (m-10) REVERT: A 635 MET cc_start: 0.8610 (tpp) cc_final: 0.8012 (tpt) REVERT: A 723 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 1203 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7436 (mmm160) REVERT: A 1207 LYS cc_start: 0.8246 (pttm) cc_final: 0.7736 (pttm) REVERT: A 1230 TRP cc_start: 0.8673 (p-90) cc_final: 0.8273 (p90) REVERT: B 52 GLU cc_start: 0.8509 (tp30) cc_final: 0.8291 (tp30) REVERT: B 230 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 344 TYR cc_start: 0.8011 (t80) cc_final: 0.7749 (t80) REVERT: B 346 LYS cc_start: 0.8462 (mttt) cc_final: 0.8202 (mttt) REVERT: B 347 ASP cc_start: 0.9099 (m-30) cc_final: 0.8807 (t0) REVERT: B 373 TYR cc_start: 0.9166 (t80) cc_final: 0.8859 (t80) REVERT: B 456 THR cc_start: 0.8688 (p) cc_final: 0.8474 (p) REVERT: B 500 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8503 (pptt) REVERT: B 556 MET cc_start: 0.7639 (tmm) cc_final: 0.7180 (tmm) REVERT: B 736 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.6181 (m-70) REVERT: B 1122 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8304 (ttt180) REVERT: B 1163 CYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 142 ILE cc_start: 0.9339 (mp) cc_final: 0.9063 (mm) REVERT: C 190 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7867 (t70) REVERT: F 111 ILE cc_start: 0.4259 (OUTLIER) cc_final: 0.3953 (pt) REVERT: F 114 GLU cc_start: 0.6836 (pm20) cc_final: 0.6620 (pm20) REVERT: F 119 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: G 13 LEU cc_start: 0.7740 (mp) cc_final: 0.7463 (mp) REVERT: G 22 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.3931 (mmm) REVERT: H 82 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7669 (mttp) REVERT: I 13 MET cc_start: 0.7587 (mmp) cc_final: 0.6867 (mtt) REVERT: I 70 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6559 (ptp90) REVERT: J 30 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: K 36 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7600 (mm-30) REVERT: L 45 SER cc_start: 0.7257 (p) cc_final: 0.6899 (t) REVERT: a 84 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.4537 (m-80) REVERT: b 44 LYS cc_start: 0.7931 (mmtm) cc_final: 0.6577 (ptmt) REVERT: b 62 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4627 (tp) REVERT: b 63 GLU cc_start: 0.5180 (tt0) cc_final: 0.4761 (mt-10) REVERT: c 109 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5383 (mt) REVERT: d 50 ILE cc_start: 0.5181 (OUTLIER) cc_final: 0.4974 (tp) REVERT: e 97 GLU cc_start: 0.5268 (mm-30) cc_final: 0.4038 (tp30) outliers start: 131 outliers final: 99 residues processed: 590 average time/residue: 0.2584 time to fit residues: 254.6792 Evaluate side-chains 607 residues out of total 3960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 490 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 819 MET Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 115 PHE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain a residue 84 PHE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 50 ILE Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 96 CYS Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 103 LEU Chi-restraints excluded: chain g residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 388 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 469 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 462 optimal weight: 20.0000 chunk 192 optimal weight: 0.0770 chunk 148 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 577 GLN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.167493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114678 restraints weight = 100119.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117703 restraints weight = 50729.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118533 restraints weight = 30383.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.119095 restraints weight = 23898.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119295 restraints weight = 20560.464| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43593 Z= 0.168 Angle : 0.657 12.060 60140 Z= 0.346 Chirality : 0.045 0.329 6759 Planarity : 0.004 0.063 6706 Dihedral : 23.049 173.677 8315 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 3.33 % Allowed : 24.49 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.02 % 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: -0.14 (0.13), residues: 4453 helix: 1.00 (0.12), residues: 1757 sheet: -0.98 (0.20), residues: 618 loop : -0.70 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG d 55 TYR 0.032 0.001 TYR E 111 PHE 0.024 0.002 PHE g 67 TRP 0.010 0.001 TRP G 79 HIS 0.006 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (43593) covalent geometry : angle 0.65732 / 0.35 (60140) hydrogen bonds : bond 0.04407 / 3.04 ( 1934) hydrogen bonds : angle 4.43182 / 3.11 ( 5251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9520.80 seconds wall clock time: 164 minutes 29.50 seconds (9869.50 seconds total)