Starting phenix.real_space_refine on Tue Aug 26 19:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5p_39777/08_2025/8z5p_39777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5p_39777/08_2025/8z5p_39777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z5p_39777/08_2025/8z5p_39777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5p_39777/08_2025/8z5p_39777.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5p_39777/08_2025/8z5p_39777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5p_39777/08_2025/8z5p_39777.cif" } resolution = 3.41 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= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 142 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 212 5.16 5 C 25604 2.51 5 N 6820 2.21 5 O 7490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40126 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7852 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 951} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 8049 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 48, 'TRANS': 952} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3065 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 356} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1097 Classifications: {'peptide': 144} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 7852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7852 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 951} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 8049 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 48, 'TRANS': 952} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3065 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 356} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1097 Classifications: {'peptide': 144} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 9.46, per 1000 atoms: 0.24 Number of scatterers: 40126 At special positions: 0 Unit cell: (171.6, 237.6, 214.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 212 16.00 O 7490 8.00 N 6820 7.00 C 25604 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: 3.43 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9440 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 37 sheets defined 58.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 23 through 26 removed outlier: 3.587A pdb=" N GLN A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.526A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 removed outlier: 3.627A pdb=" N CYS A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.562A pdb=" N VAL A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 removed outlier: 3.939A pdb=" N THR A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.953A pdb=" N VAL A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.713A pdb=" N LYS A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.981A pdb=" N VAL A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.730A pdb=" N LYS A 221 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 222 " --> pdb=" O GLY A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 258 through 263 removed outlier: 4.102A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 removed outlier: 3.727A pdb=" N VAL A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 removed outlier: 3.763A pdb=" N ILE A 336 " --> pdb=" O TRP A 332 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.702A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.540A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.982A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.558A pdb=" N LYS A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.011A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.510A pdb=" N THR A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.765A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 Processing helix chain 'A' and resid 535 through 553 removed outlier: 3.609A pdb=" N ARG A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 603 through 610 removed outlier: 4.281A pdb=" N THR A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 775 through 790 Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.676A pdb=" N TYR A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 839 through 849 removed outlier: 3.559A pdb=" N ALA A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 888 through 908 removed outlier: 3.825A pdb=" N ILE A 892 " --> pdb=" O MET A 888 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 907 " --> pdb=" O MET A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 936 Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 950 through 964 Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1095 through 1100 removed outlier: 3.830A pdb=" N GLU A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.690A pdb=" N SER A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1141 removed outlier: 3.783A pdb=" N ASP A1139 " --> pdb=" O THR A1135 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A1140 " --> pdb=" O MET A1136 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A1141 " --> pdb=" O LEU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1170 Processing helix chain 'A' and resid 1185 through 1191 removed outlier: 3.509A pdb=" N TYR A1189 " --> pdb=" O CYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1214 removed outlier: 3.900A pdb=" N TYR A1202 " --> pdb=" O GLY A1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 removed outlier: 4.052A pdb=" N LYS B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.560A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 84 through 102 Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.065A pdb=" N GLN B 132 " --> pdb=" O CYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 3.619A pdb=" N GLN B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 189 Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.940A pdb=" N VAL B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 removed outlier: 3.551A pdb=" N ASN B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 282 removed outlier: 3.753A pdb=" N HIS B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 4.286A pdb=" N CYS B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.830A pdb=" N LEU B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 removed outlier: 4.326A pdb=" N LEU B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.754A pdb=" N VAL B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 417 removed outlier: 4.079A pdb=" N VAL B 417 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.914A pdb=" N ASN B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 423 " --> pdb=" O TYR B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 433 through 436 removed outlier: 3.852A pdb=" N ARG B 436 " --> pdb=" O ASN B 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 433 through 436' Processing helix chain 'B' and resid 441 through 456 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.533A pdb=" N ILE B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.689A pdb=" N TYR B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.775A pdb=" N VAL B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.386A pdb=" N LEU B 534 " --> pdb=" O PRO B 530 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 608 Processing helix chain 'B' and resid 622 through 627 removed outlier: 4.234A pdb=" N ILE B 626 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 627 " --> pdb=" O GLU B 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 622 through 627' Processing helix chain 'B' and resid 630 through 644 removed outlier: 4.603A pdb=" N ILE B 634 " --> pdb=" O ARG B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.661A pdb=" N ILE B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 721 removed outlier: 4.606A pdb=" N ASP B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 734 Processing helix chain 'B' and resid 736 through 751 Processing helix chain 'B' and resid 762 through 777 Processing helix chain 'B' and resid 778 through 790 Processing helix chain 'B' and resid 795 through 807 removed outlier: 3.598A pdb=" N HIS B 799 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 842 Processing helix chain 'B' and resid 845 through 864 Processing helix chain 'B' and resid 865 through 869 Processing helix chain 'B' and resid 876 through 892 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.527A pdb=" N GLN B 901 " --> pdb=" O ASP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 916 Processing helix chain 'B' and resid 923 through 935 Processing helix chain 'B' and resid 940 through 951 Processing helix chain 'B' and resid 965 through 972 removed outlier: 3.717A pdb=" N MET B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 988 removed outlier: 3.798A pdb=" N SER B 980 " --> pdb=" O GLU B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1013 Processing helix chain 'B' and resid 1024 through 1044 Processing helix chain 'B' and resid 1051 through 1057 removed outlier: 3.619A pdb=" N TYR B1055 " --> pdb=" O MET B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1079 removed outlier: 3.750A pdb=" N TYR B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 removed outlier: 4.072A pdb=" N PHE C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 82 removed outlier: 4.094A pdb=" N LYS C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.834A pdb=" N TYR C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 144 removed outlier: 3.833A pdb=" N LYS C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.860A pdb=" N LEU C 191 " --> pdb=" O PRO C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.800A pdb=" N ILE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 225 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.587A pdb=" N LYS C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 300 through 324 removed outlier: 3.515A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'D' and resid 6 through 21 Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.643A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.507A pdb=" N PHE D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'E' and resid 6 through 22 Processing helix chain 'E' and resid 23 through 26 removed outlier: 3.664A pdb=" N GLN E 26 " --> pdb=" O LEU E 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 23 through 26' Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 51 through 64 removed outlier: 3.651A pdb=" N LYS E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 94 removed outlier: 3.601A pdb=" N CYS E 91 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 104 removed outlier: 3.592A pdb=" N VAL E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 152 removed outlier: 3.942A pdb=" N THR E 138 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 Processing helix chain 'E' and resid 198 through 212 removed outlier: 3.776A pdb=" N VAL E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 207 " --> pdb=" O GLY E 203 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 208 " --> pdb=" O MET E 204 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.719A pdb=" N LYS E 221 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 222 " --> pdb=" O GLY E 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 222' Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 258 through 263 removed outlier: 4.006A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 288 removed outlier: 3.767A pdb=" N VAL E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 288 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 342 removed outlier: 3.553A pdb=" N PHE E 335 " --> pdb=" O PHE E 331 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 336 " --> pdb=" O TRP E 332 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER E 342 " --> pdb=" O ASP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 3.632A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 365 No H-bonds generated for 'chain 'E' and resid 363 through 365' Processing helix chain 'E' and resid 380 through 386 removed outlier: 3.848A pdb=" N TYR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 415 Processing helix chain 'E' and resid 419 through 424 removed outlier: 4.102A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP E 424 " --> pdb=" O PRO E 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 419 through 424' Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.526A pdb=" N LYS E 458 " --> pdb=" O ILE E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.026A pdb=" N LEU E 479 " --> pdb=" O PRO E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.808A pdb=" N THR E 507 " --> pdb=" O GLY E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 526 removed outlier: 3.734A pdb=" N ILE E 525 " --> pdb=" O PRO E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 534 Processing helix chain 'E' and resid 535 through 553 removed outlier: 3.604A pdb=" N ARG E 553 " --> pdb=" O TYR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 571 removed outlier: 3.574A pdb=" N MET E 570 " --> pdb=" O SER E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 590 Processing helix chain 'E' and resid 591 through 593 No H-bonds generated for 'chain 'E' and resid 591 through 593' Processing helix chain 'E' and resid 603 through 608 Processing helix chain 'E' and resid 763 through 773 Processing helix chain 'E' and resid 775 through 790 Processing helix chain 'E' and resid 805 through 821 removed outlier: 3.576A pdb=" N TYR E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY E 815 " --> pdb=" O THR E 811 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 816 " --> pdb=" O GLU E 812 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 819 " --> pdb=" O GLY E 815 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE E 820 " --> pdb=" O LYS E 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 834 Processing helix chain 'E' and resid 839 through 850 removed outlier: 3.794A pdb=" N HIS E 850 " --> pdb=" O ASP E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 885 Processing helix chain 'E' and resid 888 through 908 removed outlier: 3.757A pdb=" N ILE E 892 " --> pdb=" O MET E 888 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG E 906 " --> pdb=" O ALA E 902 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR E 907 " --> pdb=" O MET E 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 936 Processing helix chain 'E' and resid 938 through 948 Processing helix chain 'E' and resid 950 through 964 Processing helix chain 'E' and resid 1053 through 1065 Processing helix chain 'E' and resid 1070 through 1080 Processing helix chain 'E' and resid 1095 through 1100 removed outlier: 3.682A pdb=" N GLU E1099 " --> pdb=" O SER E1095 " (cutoff:3.500A) Processing helix chain 'E' and resid 1104 through 1116 removed outlier: 4.445A pdb=" N SER E1108 " --> pdb=" O GLU E1104 " (cutoff:3.500A) Processing helix chain 'E' and resid 1120 through 1141 removed outlier: 3.892A pdb=" N ASP E1139 " --> pdb=" O THR E1135 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE E1140 " --> pdb=" O MET E1136 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1151 through 1170 Processing helix chain 'E' and resid 1185 through 1191 removed outlier: 3.669A pdb=" N TYR E1189 " --> pdb=" O CYS E1185 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1214 removed outlier: 4.052A pdb=" N TYR E1202 " --> pdb=" O GLY E1198 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 60 removed outlier: 4.109A pdb=" N LYS F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.560A pdb=" N GLN F 64 " --> pdb=" O LEU F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 84 through 102 Processing helix chain 'F' and resid 109 through 132 removed outlier: 3.559A pdb=" N LEU F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN F 132 " --> pdb=" O CYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 142 removed outlier: 3.634A pdb=" N GLN F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 189 Processing helix chain 'F' and resid 195 through 210 removed outlier: 4.046A pdb=" N VAL F 199 " --> pdb=" O ASN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 250 removed outlier: 3.536A pdb=" N VAL F 239 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 removed outlier: 3.721A pdb=" N HIS F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Proline residue: F 298 - end of helix Processing helix chain 'F' and resid 310 through 325 Processing helix chain 'F' and resid 353 through 359 removed outlier: 3.777A pdb=" N LEU F 357 " --> pdb=" O ALA F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 379 removed outlier: 4.181A pdb=" N LEU F 370 " --> pdb=" O PRO F 366 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 371 " --> pdb=" O ILE F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 396 removed outlier: 3.587A pdb=" N VAL F 385 " --> pdb=" O ASN F 381 " (cutoff:3.500A) Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 416 through 423 removed outlier: 3.514A pdb=" N GLU F 420 " --> pdb=" O PHE F 416 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS F 421 " --> pdb=" O VAL F 417 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 436 removed outlier: 3.845A pdb=" N ARG F 436 " --> pdb=" O ASN F 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 433 through 436' Processing helix chain 'F' and resid 441 through 456 Processing helix chain 'F' and resid 460 through 465 Processing helix chain 'F' and resid 472 through 476 removed outlier: 3.767A pdb=" N GLN F 476 " --> pdb=" O LEU F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 513 removed outlier: 3.678A pdb=" N TYR F 513 " --> pdb=" O PHE F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 523 removed outlier: 3.723A pdb=" N VAL F 523 " --> pdb=" O PRO F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 541 removed outlier: 4.356A pdb=" N LEU F 534 " --> pdb=" O PRO F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 563 Processing helix chain 'F' and resid 586 through 589 Processing helix chain 'F' and resid 590 through 608 Processing helix chain 'F' and resid 622 through 627 removed outlier: 4.223A pdb=" N ILE F 626 " --> pdb=" O ARG F 622 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 622 through 627' Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 631 through 644 removed outlier: 3.521A pdb=" N LEU F 635 " --> pdb=" O PHE F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 661 Processing helix chain 'F' and resid 669 through 674 removed outlier: 3.957A pdb=" N ILE F 673 " --> pdb=" O ASP F 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 721 removed outlier: 4.606A pdb=" N ASP F 721 " --> pdb=" O SER F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 734 Processing helix chain 'F' and resid 736 through 751 Processing helix chain 'F' and resid 762 through 777 Processing helix chain 'F' and resid 778 through 790 Processing helix chain 'F' and resid 795 through 807 removed outlier: 3.576A pdb=" N HIS F 799 " --> pdb=" O SER F 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 842 Processing helix chain 'F' and resid 845 through 864 Processing helix chain 'F' and resid 865 through 869 Processing helix chain 'F' and resid 876 through 892 Processing helix chain 'F' and resid 898 through 902 Processing helix chain 'F' and resid 903 through 916 Processing helix chain 'F' and resid 923 through 934 Processing helix chain 'F' and resid 940 through 951 Processing helix chain 'F' and resid 965 through 972 Processing helix chain 'F' and resid 976 through 988 removed outlier: 3.843A pdb=" N SER F 980 " --> pdb=" O GLU F 976 " (cutoff:3.500A) Processing helix chain 'F' and resid 992 through 1013 Processing helix chain 'F' and resid 1024 through 1044 Processing helix chain 'F' and resid 1051 through 1057 Processing helix chain 'F' and resid 1064 through 1079 removed outlier: 3.736A pdb=" N TYR F1068 " --> pdb=" O GLY F1064 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 19 removed outlier: 4.241A pdb=" N PHE G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'G' and resid 60 through 82 removed outlier: 3.778A pdb=" N LYS G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL G 81 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 removed outlier: 3.811A pdb=" N TYR G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 144 removed outlier: 3.510A pdb=" N THR G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS G 129 " --> pdb=" O LYS G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 192 through 201 Processing helix chain 'G' and resid 209 through 226 Processing helix chain 'G' and resid 234 through 245 Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.821A pdb=" N TRP G 254 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 269 removed outlier: 3.685A pdb=" N LYS G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 284 Processing helix chain 'G' and resid 285 through 289 Processing helix chain 'G' and resid 300 through 324 removed outlier: 3.525A pdb=" N LYS G 304 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR G 319 " --> pdb=" O SER G 315 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR G 320 " --> pdb=" O VAL G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 336 Processing helix chain 'G' and resid 340 through 355 Processing helix chain 'G' and resid 366 through 370 Processing helix chain 'G' and resid 377 through 382 Processing helix chain 'H' and resid 6 through 21 Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.518A pdb=" N GLY H 41 " --> pdb=" O MET H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 94 Processing helix chain 'H' and resid 102 through 114 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.195A pdb=" N LEU A 372 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 563 removed outlier: 3.872A pdb=" N GLY A 602 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.309A pdb=" N ARG A 472 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 853 through 855 removed outlier: 6.547A pdb=" N HIS A 853 " --> pdb=" O LEU A 918 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.629A pdb=" N LEU A1085 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY A1084 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.934A pdb=" N ALA B 82 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 153 " --> pdb=" O ALA B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB3, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AB4, first strand: chain 'B' and resid 616 through 620 removed outlier: 4.274A pdb=" N ASP B 654 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 499 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 527 through 528 removed outlier: 6.634A pdb=" N GLN B 527 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 756 through 757 Processing sheet with id=AB7, first strand: chain 'B' and resid 819 through 822 removed outlier: 3.597A pdb=" N ILE B 822 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 810 " --> pdb=" O ILE B 822 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN B 809 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 961 through 964 removed outlier: 3.640A pdb=" N LEU B 963 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 956 " --> pdb=" O LEU B 963 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B1022 " --> pdb=" O GLY B 955 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE B 957 " --> pdb=" O VAL B1022 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 20 through 28 removed outlier: 6.441A pdb=" N ILE C 38 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU C 24 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 36 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 34 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG C 28 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 33 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 50 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 92 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.679A pdb=" N VAL C 147 " --> pdb=" O CYS C 173 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 173 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 156 through 158 removed outlier: 3.892A pdb=" N LEU C 157 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 165 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'E' and resid 360 through 361 removed outlier: 3.551A pdb=" N ILE E 360 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 372 through 374 removed outlier: 4.204A pdb=" N LEU E 372 " --> pdb=" O MET E 395 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 561 through 563 Processing sheet with id=AC7, first strand: chain 'E' and resid 445 through 446 Processing sheet with id=AC8, first strand: chain 'E' and resid 471 through 474 removed outlier: 6.386A pdb=" N ARG E 472 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR E 511 " --> pdb=" O PHE E 518 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AD1, first strand: chain 'E' and resid 1085 through 1086 Processing sheet with id=AD2, first strand: chain 'F' and resid 397 through 398 Processing sheet with id=AD3, first strand: chain 'F' and resid 410 through 411 Processing sheet with id=AD4, first strand: chain 'F' and resid 616 through 620 removed outlier: 3.567A pdb=" N VAL F 495 " --> pdb=" O LYS F 650 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP F 654 " --> pdb=" O VAL F 497 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU F 499 " --> pdb=" O ASP F 654 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 527 through 528 removed outlier: 6.795A pdb=" N GLN F 527 " --> pdb=" O VAL F 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 756 through 757 Processing sheet with id=AD7, first strand: chain 'F' and resid 819 through 822 removed outlier: 4.516A pdb=" N VAL F 810 " --> pdb=" O ILE F 822 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN F 809 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 961 through 964 removed outlier: 3.586A pdb=" N LEU F 963 " --> pdb=" O ILE F 956 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE F 956 " --> pdb=" O LEU F 963 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL F1022 " --> pdb=" O GLY F 955 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE F 957 " --> pdb=" O VAL F1022 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 20 through 28 removed outlier: 6.447A pdb=" N ILE G 38 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU G 24 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 36 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL G 34 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG G 28 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL G 33 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL G 50 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP G 92 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 146 through 147 removed outlier: 3.650A pdb=" N VAL G 147 " --> pdb=" O CYS G 173 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS G 173 " --> pdb=" O VAL G 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 1909 hydrogen bonds defined for protein. 5532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8908 1.33 - 1.46: 11211 1.46 - 1.59: 20508 1.59 - 1.72: 3 1.72 - 1.84: 344 Bond restraints: 40974 Sorted by residual: bond pdb=" N ILE F 300 " pdb=" CA ILE F 300 " ideal model delta sigma weight residual 1.456 1.412 0.044 1.09e-02 8.42e+03 1.62e+01 bond pdb=" CA CYS F 299 " pdb=" C CYS F 299 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.35e+01 bond pdb=" C LEU F 297 " pdb=" O LEU F 297 " ideal model delta sigma weight residual 1.244 1.213 0.031 1.00e-02 1.00e+04 9.51e+00 bond pdb=" C ILE F 300 " pdb=" N SER F 301 " ideal model delta sigma weight residual 1.328 1.301 0.027 8.90e-03 1.26e+04 9.15e+00 bond pdb=" CG PRO G 286 " pdb=" CD PRO G 286 " ideal model delta sigma weight residual 1.503 1.401 0.102 3.40e-02 8.65e+02 8.97e+00 ... (remaining 40969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 55238 3.48 - 6.97: 216 6.97 - 10.45: 42 10.45 - 13.93: 3 13.93 - 17.42: 1 Bond angle restraints: 55500 Sorted by residual: angle pdb=" CA PRO A 862 " pdb=" N PRO A 862 " pdb=" CD PRO A 862 " ideal model delta sigma weight residual 111.50 94.08 17.42 1.40e+00 5.10e-01 1.55e+02 angle pdb=" N ILE F 300 " pdb=" CA ILE F 300 " pdb=" C ILE F 300 " ideal model delta sigma weight residual 111.88 103.48 8.40 1.06e+00 8.90e-01 6.29e+01 angle pdb=" CA PRO A 224 " pdb=" N PRO A 224 " pdb=" CD PRO A 224 " ideal model delta sigma weight residual 112.00 101.74 10.26 1.40e+00 5.10e-01 5.37e+01 angle pdb=" CA PRO G 286 " pdb=" N PRO G 286 " pdb=" CD PRO G 286 " ideal model delta sigma weight residual 112.00 102.29 9.71 1.40e+00 5.10e-01 4.81e+01 angle pdb=" CA PRO B 284 " pdb=" N PRO B 284 " pdb=" CD PRO B 284 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 ... (remaining 55495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20921 17.98 - 35.96: 2817 35.96 - 53.94: 836 53.94 - 71.91: 124 71.91 - 89.89: 74 Dihedral angle restraints: 24772 sinusoidal: 10106 harmonic: 14666 Sorted by residual: dihedral pdb=" CA LEU F 778 " pdb=" C LEU F 778 " pdb=" N TRP F 779 " pdb=" CA TRP F 779 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU E 398 " pdb=" C LEU E 398 " pdb=" N PRO E 399 " pdb=" CA PRO E 399 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA MET C 241 " pdb=" C MET C 241 " pdb=" N ILE C 242 " pdb=" CA ILE C 242 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 24769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5481 0.063 - 0.125: 695 0.125 - 0.188: 24 0.188 - 0.250: 4 0.250 - 0.313: 2 Chirality restraints: 6206 Sorted by residual: chirality pdb=" CG LEU B 549 " pdb=" CB LEU B 549 " pdb=" CD1 LEU B 549 " pdb=" CD2 LEU B 549 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CG LEU C 310 " pdb=" CB LEU C 310 " pdb=" CD1 LEU C 310 " pdb=" CD2 LEU C 310 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA LEU F 297 " pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CB LEU F 297 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 6203 not shown) Planarity restraints: 7148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 861 " 0.106 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO A 862 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 251 " 0.088 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO G 252 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO G 252 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO G 252 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 223 " -0.087 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO A 224 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " -0.066 5.00e-02 4.00e+02 ... (remaining 7145 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 899 2.70 - 3.25: 39730 3.25 - 3.80: 61814 3.80 - 4.35: 73528 4.35 - 4.90: 124159 Nonbonded interactions: 300130 Sorted by model distance: nonbonded pdb=" O PHE C 169 " pdb=" OG SER C 172 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR E 814 " pdb=" OG SER E 830 " model vdw 2.174 3.040 nonbonded pdb=" O LYS A 319 " pdb=" OH TYR A 384 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A1142 " pdb=" ND1 HIS A1143 " model vdw 2.197 3.120 nonbonded pdb=" O VAL G 218 " pdb=" OG1 THR G 222 " model vdw 2.216 3.040 ... (remaining 300125 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.680 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 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 : 0.003 0.135 40974 Z= 0.138 Angle : 0.633 17.417 55500 Z= 0.334 Chirality : 0.040 0.313 6206 Planarity : 0.005 0.145 7148 Dihedral : 18.147 89.892 15332 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 0.30 % Allowed : 24.15 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.12), residues: 5004 helix: 2.20 (0.10), residues: 2566 sheet: 1.20 (0.39), residues: 158 loop : -0.84 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 36 TYR 0.030 0.001 TYR B 328 PHE 0.065 0.001 PHE D 66 TRP 0.034 0.001 TRP A1054 HIS 0.020 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00288 (40974) covalent geometry : angle 0.63345 (55500) hydrogen bonds : bond 0.14954 ( 1909) hydrogen bonds : angle 4.85250 ( 5532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 385 time to evaluate : 1.766 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 TYR cc_start: 0.6909 (t80) cc_final: 0.6641 (t80) REVERT: B 349 TYR cc_start: 0.5454 (m-10) cc_final: 0.5062 (m-10) REVERT: E 927 MET cc_start: 0.1809 (mtt) cc_final: 0.1523 (mtt) REVERT: G 241 MET cc_start: 0.4872 (mtt) cc_final: 0.3955 (tpt) outliers start: 13 outliers final: 4 residues processed: 396 average time/residue: 0.2241 time to fit residues: 153.9536 Evaluate side-chains 375 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 371 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 475 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 239 GLN A 895 GLN B 64 GLN ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 228 ASN B 229 ASN B 258 GLN B 398 HIS ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 ASN B 935 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS E 147 GLN E 191 ASN ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN F 496 HIS F 657 GLN F 916 GLN G 39 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.228237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190476 restraints weight = 77298.045| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.35 r_work: 0.3780 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 40974 Z= 0.316 Angle : 0.868 13.690 55500 Z= 0.454 Chirality : 0.051 0.236 6206 Planarity : 0.006 0.079 7148 Dihedral : 5.026 55.460 5502 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.71 % Favored : 93.09 % Rotamer: Outliers : 4.75 % Allowed : 21.44 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.01 (0.12), residues: 5004 helix: 1.27 (0.10), residues: 2562 sheet: 0.43 (0.40), residues: 146 loop : -1.55 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 429 TYR 0.053 0.003 TYR F 403 PHE 0.049 0.003 PHE G 268 TRP 0.052 0.003 TRP A 328 HIS 0.025 0.002 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00746 (40974) covalent geometry : angle 0.86821 (55500) hydrogen bonds : bond 0.08243 ( 1909) hydrogen bonds : angle 4.70923 ( 5532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 436 time to evaluate : 1.688 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 463 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: A 537 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7292 (pttm) REVERT: A 1123 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: A 1200 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.4725 (mpt) REVERT: A 1205 LYS cc_start: 0.7475 (mtmt) cc_final: 0.7188 (pttm) REVERT: B 198 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6259 (mt-10) REVERT: B 416 PHE cc_start: 0.6681 (m-80) cc_final: 0.6470 (m-10) REVERT: B 538 TYR cc_start: 0.8343 (m-10) cc_final: 0.8032 (m-80) REVERT: B 549 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7169 (mp) REVERT: B 571 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7725 (mtmm) REVERT: B 853 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7194 (tp) REVERT: B 918 GLN cc_start: 0.2445 (OUTLIER) cc_final: 0.2188 (mm-40) REVERT: C 238 MET cc_start: 0.5427 (ttt) cc_final: 0.4939 (ttt) REVERT: D 138 ASN cc_start: 0.7390 (t0) cc_final: 0.6971 (t0) REVERT: E 61 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6788 (t80) REVERT: E 79 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: E 341 PHE cc_start: 0.2726 (OUTLIER) cc_final: 0.1524 (t80) REVERT: E 401 MET cc_start: 0.6730 (tpp) cc_final: 0.5889 (ttm) REVERT: E 448 THR cc_start: 0.3193 (OUTLIER) cc_final: 0.2982 (t) REVERT: E 555 ARG cc_start: 0.6202 (tpp80) cc_final: 0.5998 (mmp-170) REVERT: E 814 TYR cc_start: 0.3516 (OUTLIER) cc_final: 0.1857 (t80) REVERT: E 823 TRP cc_start: 0.4896 (m100) cc_final: 0.4586 (m100) REVERT: E 1100 MET cc_start: 0.3356 (mmm) cc_final: 0.3119 (mmm) REVERT: F 153 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6850 (p90) REVERT: F 198 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: F 332 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6358 (mtp85) REVERT: F 779 TRP cc_start: 0.6089 (m-90) cc_final: 0.5859 (m-90) REVERT: F 878 TRP cc_start: 0.5185 (m100) cc_final: 0.4884 (m100) REVERT: G 126 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5802 (tp30) REVERT: G 162 MET cc_start: 0.4662 (mmt) cc_final: 0.4392 (mmt) REVERT: G 299 PHE cc_start: -0.1720 (OUTLIER) cc_final: -0.2140 (t80) REVERT: H 25 ASP cc_start: 0.5747 (p0) cc_final: 0.5537 (p0) REVERT: H 136 GLN cc_start: 0.1247 (OUTLIER) cc_final: -0.0014 (tm-30) outliers start: 209 outliers final: 92 residues processed: 610 average time/residue: 0.2302 time to fit residues: 238.8460 Evaluate side-chains 461 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 349 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 262 TRP Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 918 GLN Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1051 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 570 MET Chi-restraints excluded: chain E residue 619 MET Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 262 TRP Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 360 LYS Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 171 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 391 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 359 optimal weight: 0.5980 chunk 472 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 528 GLN A 850 HIS A 933 HIS ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS E 822 HIS F 195 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.232374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.195302 restraints weight = 77341.791| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.31 r_work: 0.3848 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40974 Z= 0.127 Angle : 0.591 10.386 55500 Z= 0.306 Chirality : 0.041 0.184 6206 Planarity : 0.004 0.068 7148 Dihedral : 4.306 56.900 5498 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.60 % Favored : 94.24 % Rotamer: Outliers : 3.05 % Allowed : 23.90 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.56 (0.12), residues: 5004 helix: 1.82 (0.10), residues: 2552 sheet: 0.88 (0.42), residues: 136 loop : -1.39 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 917 TYR 0.024 0.001 TYR F 576 PHE 0.038 0.001 PHE G 268 TRP 0.014 0.001 TRP E 554 HIS 0.009 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00270 (40974) covalent geometry : angle 0.59079 (55500) hydrogen bonds : bond 0.04605 ( 1909) hydrogen bonds : angle 4.09193 ( 5532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 390 time to evaluate : 1.623 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: symmetry clash REVERT: A 537 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7129 (ptpp) REVERT: A 1123 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: A 1200 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.4649 (mpt) REVERT: A 1205 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7132 (pttm) REVERT: B 571 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7680 (mtmm) REVERT: B 596 ASP cc_start: 0.7294 (m-30) cc_final: 0.6738 (t0) REVERT: D 138 ASN cc_start: 0.7444 (t0) cc_final: 0.7032 (t0) REVERT: E 61 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6762 (t80) REVERT: E 341 PHE cc_start: 0.2833 (OUTLIER) cc_final: 0.1711 (t80) REVERT: E 395 MET cc_start: 0.7218 (tpp) cc_final: 0.6770 (tpp) REVERT: E 401 MET cc_start: 0.6459 (tpp) cc_final: 0.5909 (ttm) REVERT: E 448 THR cc_start: 0.3130 (OUTLIER) cc_final: 0.2782 (t) REVERT: E 474 GLN cc_start: 0.5038 (pm20) cc_final: 0.4792 (pm20) REVERT: E 481 HIS cc_start: 0.3632 (OUTLIER) cc_final: 0.3214 (t70) REVERT: E 589 MET cc_start: 0.6427 (mmt) cc_final: 0.5895 (mmm) REVERT: E 814 TYR cc_start: 0.3943 (OUTLIER) cc_final: 0.1974 (t80) REVERT: F 101 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7766 (t80) REVERT: F 153 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6406 (p90) REVERT: F 286 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7576 (tm-30) REVERT: G 108 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5705 (mtmm) REVERT: H 25 ASP cc_start: 0.5662 (p0) cc_final: 0.5394 (p0) REVERT: H 136 GLN cc_start: 0.0922 (OUTLIER) cc_final: -0.0272 (tm-30) outliers start: 134 outliers final: 61 residues processed: 495 average time/residue: 0.2286 time to fit residues: 192.7909 Evaluate side-chains 423 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 349 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1051 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 481 HIS Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 848 LEU Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 260 CYS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 458 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 336 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 291 ASN B 381 ASN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS E 851 GLN E 960 HIS F 51 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.228628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.191856 restraints weight = 78461.860| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.35 r_work: 0.3798 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 40974 Z= 0.177 Angle : 0.640 10.505 55500 Z= 0.330 Chirality : 0.043 0.192 6206 Planarity : 0.005 0.063 7148 Dihedral : 4.405 55.505 5498 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.63 % Favored : 93.21 % Rotamer: Outliers : 3.80 % Allowed : 23.62 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.38 (0.12), residues: 5004 helix: 1.69 (0.10), residues: 2564 sheet: 0.63 (0.40), residues: 146 loop : -1.54 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 332 TYR 0.025 0.002 TYR F 403 PHE 0.037 0.002 PHE G 268 TRP 0.023 0.002 TRP A 328 HIS 0.020 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00409 (40974) covalent geometry : angle 0.64020 (55500) hydrogen bonds : bond 0.05565 ( 1909) hydrogen bonds : angle 4.13974 ( 5532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 375 time to evaluate : 1.658 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 469 TYR cc_start: 0.6618 (t80) cc_final: 0.6358 (t80) REVERT: A 537 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7143 (ptpp) REVERT: A 1123 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: A 1200 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.4990 (mpt) REVERT: A 1205 LYS cc_start: 0.7453 (mtmt) cc_final: 0.7139 (pttm) REVERT: B 198 GLU cc_start: 0.6481 (mp0) cc_final: 0.5858 (mp0) REVERT: B 338 TYR cc_start: 0.5906 (t80) cc_final: 0.5599 (t80) REVERT: B 571 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7926 (mtmm) REVERT: B 596 ASP cc_start: 0.7450 (m-30) cc_final: 0.6710 (t0) REVERT: B 598 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.6901 (mt) REVERT: B 845 ARG cc_start: 0.4723 (mtm-85) cc_final: 0.4452 (mmm160) REVERT: B 853 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7287 (tp) REVERT: B 883 MET cc_start: 0.7154 (ptm) cc_final: 0.6952 (ptm) REVERT: C 238 MET cc_start: 0.5240 (ttt) cc_final: 0.4944 (ttt) REVERT: D 125 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5379 (tpp) REVERT: D 138 ASN cc_start: 0.7417 (t0) cc_final: 0.7017 (t0) REVERT: E 61 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6846 (t80) REVERT: E 103 LYS cc_start: 0.5762 (OUTLIER) cc_final: 0.5285 (tptm) REVERT: E 341 PHE cc_start: 0.3218 (OUTLIER) cc_final: 0.1891 (t80) REVERT: E 378 ASP cc_start: 0.7358 (p0) cc_final: 0.6953 (p0) REVERT: E 401 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6360 (mtt) REVERT: E 448 THR cc_start: 0.3186 (OUTLIER) cc_final: 0.2893 (t) REVERT: E 474 GLN cc_start: 0.5323 (pm20) cc_final: 0.4954 (pm20) REVERT: E 589 MET cc_start: 0.6679 (mmt) cc_final: 0.6141 (mmm) REVERT: E 814 TYR cc_start: 0.3687 (OUTLIER) cc_final: 0.1670 (t80) REVERT: E 822 HIS cc_start: 0.5800 (t70) cc_final: 0.4929 (m170) REVERT: E 900 TYR cc_start: 0.6125 (m-80) cc_final: 0.5922 (m-80) REVERT: F 88 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8036 (mt) REVERT: F 101 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8058 (t80) REVERT: F 153 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.6092 (p90) REVERT: F 198 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: F 286 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7481 (tm-30) REVERT: F 638 LEU cc_start: 0.7713 (tt) cc_final: 0.7458 (mt) REVERT: F 883 MET cc_start: 0.6336 (mtm) cc_final: 0.6117 (mtm) REVERT: G 123 SER cc_start: 0.2129 (OUTLIER) cc_final: 0.1107 (m) REVERT: G 126 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5657 (tp30) REVERT: G 241 MET cc_start: 0.4996 (mtt) cc_final: 0.4653 (mtp) REVERT: G 299 PHE cc_start: -0.1829 (OUTLIER) cc_final: -0.2199 (t80) REVERT: H 136 GLN cc_start: 0.1435 (OUTLIER) cc_final: -0.0068 (tm-30) outliers start: 167 outliers final: 96 residues processed: 499 average time/residue: 0.2321 time to fit residues: 197.8461 Evaluate side-chains 458 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 341 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 570 MET Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 260 CYS Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 303 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 248 optimal weight: 0.4980 chunk 15 optimal weight: 0.0030 chunk 158 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 381 ASN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS E 960 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.231053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.194476 restraints weight = 78906.089| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.31 r_work: 0.3848 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40974 Z= 0.113 Angle : 0.566 10.507 55500 Z= 0.288 Chirality : 0.041 0.152 6206 Planarity : 0.004 0.062 7148 Dihedral : 4.127 54.770 5496 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 2.80 % Allowed : 25.08 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.70 (0.12), residues: 5004 helix: 1.98 (0.10), residues: 2550 sheet: 1.01 (0.42), residues: 136 loop : -1.39 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 555 TYR 0.018 0.001 TYR B 53 PHE 0.040 0.001 PHE G 268 TRP 0.019 0.001 TRP E 554 HIS 0.012 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00240 (40974) covalent geometry : angle 0.56578 (55500) hydrogen bonds : bond 0.03942 ( 1909) hydrogen bonds : angle 3.88418 ( 5532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 375 time to evaluate : 1.624 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 411 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7605 (p) REVERT: A 1123 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: A 1205 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7145 (pttm) REVERT: B 198 GLU cc_start: 0.6450 (mp0) cc_final: 0.5821 (mp0) REVERT: B 338 TYR cc_start: 0.5836 (t80) cc_final: 0.5590 (t80) REVERT: B 571 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7904 (mtmm) REVERT: B 596 ASP cc_start: 0.7403 (m-30) cc_final: 0.6592 (t0) REVERT: B 853 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7231 (tp) REVERT: C 241 MET cc_start: 0.8690 (pmm) cc_final: 0.8212 (tpp) REVERT: D 125 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5338 (tpp) REVERT: D 138 ASN cc_start: 0.7635 (t0) cc_final: 0.7323 (t0) REVERT: E 341 PHE cc_start: 0.2994 (OUTLIER) cc_final: 0.1536 (t80) REVERT: E 378 ASP cc_start: 0.7424 (p0) cc_final: 0.7077 (p0) REVERT: E 474 GLN cc_start: 0.5147 (pm20) cc_final: 0.4785 (pm20) REVERT: E 555 ARG cc_start: 0.6385 (mmp-170) cc_final: 0.5084 (mmt-90) REVERT: E 568 HIS cc_start: 0.5104 (OUTLIER) cc_final: 0.4161 (t-90) REVERT: E 589 MET cc_start: 0.6487 (mmt) cc_final: 0.6034 (mmm) REVERT: E 814 TYR cc_start: 0.3886 (OUTLIER) cc_final: 0.2022 (t80) REVERT: E 822 HIS cc_start: 0.5954 (t70) cc_final: 0.4914 (m170) REVERT: E 900 TYR cc_start: 0.5983 (m-80) cc_final: 0.5650 (m-80) REVERT: F 101 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7686 (t80) REVERT: F 153 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6173 (p90) REVERT: F 198 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6269 (mt-10) REVERT: F 286 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7388 (tm-30) REVERT: F 481 MET cc_start: 0.6710 (tpp) cc_final: 0.6066 (ttt) REVERT: F 611 MET cc_start: 0.8083 (mmm) cc_final: 0.7880 (mmp) REVERT: F 637 MET cc_start: 0.6024 (tmm) cc_final: 0.4189 (ptm) REVERT: F 638 LEU cc_start: 0.7649 (tt) cc_final: 0.7356 (mt) REVERT: G 66 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: G 126 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5762 (tp30) REVERT: G 166 LEU cc_start: 0.6925 (tp) cc_final: 0.6644 (tp) REVERT: G 241 MET cc_start: 0.5191 (mtt) cc_final: 0.4921 (mtp) REVERT: G 299 PHE cc_start: -0.1484 (OUTLIER) cc_final: -0.1952 (t80) REVERT: H 25 ASP cc_start: 0.5180 (p0) cc_final: 0.4949 (p0) REVERT: H 136 GLN cc_start: 0.1271 (OUTLIER) cc_final: -0.0113 (tm-30) outliers start: 123 outliers final: 68 residues processed: 467 average time/residue: 0.2321 time to fit residues: 185.1471 Evaluate side-chains 431 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 348 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1051 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 568 HIS Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 743 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 498 optimal weight: 2.9990 chunk 319 optimal weight: 0.4980 chunk 363 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 467 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 129 optimal weight: 0.0070 chunk 245 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 381 ASN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.230969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.193446 restraints weight = 79204.541| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.40 r_work: 0.3848 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40974 Z= 0.112 Angle : 0.561 10.516 55500 Z= 0.285 Chirality : 0.040 0.162 6206 Planarity : 0.004 0.062 7148 Dihedral : 4.019 54.538 5496 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.67 % Rotamer: Outliers : 3.00 % Allowed : 24.76 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.77 (0.12), residues: 5004 helix: 2.04 (0.10), residues: 2560 sheet: 0.93 (0.41), residues: 136 loop : -1.37 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 845 TYR 0.019 0.001 TYR B 53 PHE 0.037 0.001 PHE G 268 TRP 0.015 0.001 TRP E 554 HIS 0.030 0.001 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00242 (40974) covalent geometry : angle 0.56098 (55500) hydrogen bonds : bond 0.03913 ( 1909) hydrogen bonds : angle 3.81624 ( 5532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 375 time to evaluate : 1.630 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 411 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7583 (p) REVERT: A 1123 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6335 (m-80) REVERT: A 1200 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.4914 (mpt) REVERT: B 144 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7113 (ttp80) REVERT: B 198 GLU cc_start: 0.6415 (mp0) cc_final: 0.6131 (mp0) REVERT: B 338 TYR cc_start: 0.5762 (t80) cc_final: 0.5517 (t80) REVERT: B 538 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 596 ASP cc_start: 0.7395 (m-30) cc_final: 0.6578 (t0) REVERT: B 804 LEU cc_start: 0.4525 (tp) cc_final: 0.4095 (pp) REVERT: B 853 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7268 (tp) REVERT: D 125 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5332 (tpp) REVERT: E 103 LYS cc_start: 0.5224 (OUTLIER) cc_final: 0.4954 (tptm) REVERT: E 341 PHE cc_start: 0.2968 (OUTLIER) cc_final: 0.1447 (t80) REVERT: E 378 ASP cc_start: 0.7525 (p0) cc_final: 0.7274 (p0) REVERT: E 474 GLN cc_start: 0.5222 (pm20) cc_final: 0.4870 (pm20) REVERT: E 589 MET cc_start: 0.6617 (mmt) cc_final: 0.6139 (mmm) REVERT: E 785 MET cc_start: 0.1318 (tmm) cc_final: 0.0696 (tpp) REVERT: E 814 TYR cc_start: 0.3781 (OUTLIER) cc_final: 0.1905 (t80) REVERT: E 822 HIS cc_start: 0.6144 (t70) cc_final: 0.5143 (m170) REVERT: F 101 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7656 (t80) REVERT: F 122 MET cc_start: 0.8266 (mmm) cc_final: 0.7975 (mmt) REVERT: F 153 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6293 (p90) REVERT: F 198 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6224 (mt-10) REVERT: F 286 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7339 (tm-30) REVERT: F 481 MET cc_start: 0.6849 (tpp) cc_final: 0.6138 (ttt) REVERT: F 638 LEU cc_start: 0.7673 (tt) cc_final: 0.7434 (mt) REVERT: G 66 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: G 126 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5783 (tp30) REVERT: G 166 LEU cc_start: 0.6849 (tp) cc_final: 0.6605 (tp) REVERT: G 299 PHE cc_start: -0.1676 (OUTLIER) cc_final: -0.1956 (t80) REVERT: H 136 GLN cc_start: 0.1078 (OUTLIER) cc_final: -0.0306 (tm-30) outliers start: 132 outliers final: 81 residues processed: 476 average time/residue: 0.2368 time to fit residues: 190.5846 Evaluate side-chains 444 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 346 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 848 LEU Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 743 LEU Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 454 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 390 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 184 optimal weight: 0.0050 chunk 99 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS F 51 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.229551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.196220 restraints weight = 78937.760| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.19 r_work: 0.3938 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40974 Z= 0.132 Angle : 0.585 10.572 55500 Z= 0.298 Chirality : 0.041 0.181 6206 Planarity : 0.004 0.070 7148 Dihedral : 4.081 53.668 5496 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.47 % Favored : 93.39 % Rotamer: Outliers : 3.23 % Allowed : 24.69 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.68 (0.12), residues: 5004 helix: 1.95 (0.10), residues: 2556 sheet: 0.93 (0.41), residues: 136 loop : -1.40 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 845 TYR 0.023 0.001 TYR B 53 PHE 0.040 0.001 PHE G 268 TRP 0.018 0.001 TRP A 328 HIS 0.015 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00293 (40974) covalent geometry : angle 0.58548 (55500) hydrogen bonds : bond 0.04393 ( 1909) hydrogen bonds : angle 3.90182 ( 5532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 361 time to evaluate : 1.626 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 105 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7308 (p) REVERT: A 359 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7259 (mp) REVERT: A 411 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7637 (p) REVERT: A 537 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7269 (pttm) REVERT: A 914 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6953 (mt-10) REVERT: A 1200 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.5194 (mpt) REVERT: B 144 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7339 (ttp80) REVERT: B 338 TYR cc_start: 0.5974 (t80) cc_final: 0.5734 (t80) REVERT: B 341 SER cc_start: 0.6140 (OUTLIER) cc_final: 0.5867 (m) REVERT: B 538 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: B 596 ASP cc_start: 0.7137 (m-30) cc_final: 0.6482 (t0) REVERT: B 804 LEU cc_start: 0.4563 (tp) cc_final: 0.4220 (pp) REVERT: B 820 GLU cc_start: 0.6051 (mp0) cc_final: 0.4085 (mm-30) REVERT: B 853 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7383 (tp) REVERT: C 241 MET cc_start: 0.8433 (pmm) cc_final: 0.8004 (tpp) REVERT: D 73 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5250 (mpp) REVERT: D 125 MET cc_start: 0.5501 (OUTLIER) cc_final: 0.5022 (tpp) REVERT: E 61 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7531 (t80) REVERT: E 103 LYS cc_start: 0.5730 (OUTLIER) cc_final: 0.5112 (tptm) REVERT: E 341 PHE cc_start: 0.3145 (OUTLIER) cc_final: 0.1330 (t80) REVERT: E 378 ASP cc_start: 0.6953 (p0) cc_final: 0.6678 (p0) REVERT: E 474 GLN cc_start: 0.5398 (pm20) cc_final: 0.5032 (pm20) REVERT: E 589 MET cc_start: 0.6874 (mmt) cc_final: 0.6417 (mmm) REVERT: E 785 MET cc_start: 0.1477 (tmm) cc_final: 0.0856 (tpp) REVERT: E 814 TYR cc_start: 0.3428 (OUTLIER) cc_final: 0.1309 (t80) REVERT: E 822 HIS cc_start: 0.6165 (t70) cc_final: 0.5433 (m170) REVERT: F 101 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7659 (t80) REVERT: F 153 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6207 (p90) REVERT: F 198 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6345 (mt-10) REVERT: F 286 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 481 MET cc_start: 0.6606 (tpp) cc_final: 0.5832 (ttt) REVERT: G 123 SER cc_start: 0.2642 (OUTLIER) cc_final: 0.2008 (m) REVERT: G 126 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5576 (tp30) REVERT: H 136 GLN cc_start: 0.2059 (OUTLIER) cc_final: 0.0035 (tm-30) outliers start: 142 outliers final: 84 residues processed: 466 average time/residue: 0.2345 time to fit residues: 186.1329 Evaluate side-chains 450 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 345 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 164 TYR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 743 LEU Chi-restraints excluded: chain F residue 853 LEU Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 388 optimal weight: 2.9990 chunk 445 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 474 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 253 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS F 51 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.228928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.195388 restraints weight = 78447.997| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.06 r_work: 0.3899 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40974 Z= 0.133 Angle : 0.603 15.785 55500 Z= 0.306 Chirality : 0.041 0.262 6206 Planarity : 0.004 0.065 7148 Dihedral : 4.116 53.229 5496 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.37 % Favored : 93.47 % Rotamer: Outliers : 3.14 % Allowed : 25.03 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.61 (0.12), residues: 5004 helix: 1.89 (0.10), residues: 2560 sheet: 0.92 (0.42), residues: 136 loop : -1.42 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 655 TYR 0.024 0.001 TYR B 53 PHE 0.041 0.001 PHE G 268 TRP 0.018 0.001 TRP A 328 HIS 0.015 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00300 (40974) covalent geometry : angle 0.60319 (55500) hydrogen bonds : bond 0.04406 ( 1909) hydrogen bonds : angle 3.93627 ( 5532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 349 time to evaluate : 1.633 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 105 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7505 (p) REVERT: A 411 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 502 MET cc_start: 0.8560 (mmt) cc_final: 0.8313 (mmt) REVERT: A 537 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7266 (pttm) REVERT: A 1123 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6249 (m-80) REVERT: A 1200 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.5197 (mpt) REVERT: A 1205 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5034 (tttm) REVERT: B 144 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7257 (ttp80) REVERT: B 341 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.6165 (m) REVERT: B 538 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: B 596 ASP cc_start: 0.7159 (m-30) cc_final: 0.6481 (t0) REVERT: B 804 LEU cc_start: 0.4484 (tp) cc_final: 0.4122 (pp) REVERT: C 162 MET cc_start: 0.7740 (mmm) cc_final: 0.7418 (mmm) REVERT: C 241 MET cc_start: 0.8664 (pmm) cc_final: 0.8211 (tpp) REVERT: D 73 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5242 (mpp) REVERT: D 125 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5099 (tpp) REVERT: E 61 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7925 (t80) REVERT: E 103 LYS cc_start: 0.5594 (OUTLIER) cc_final: 0.4996 (tptm) REVERT: E 305 LYS cc_start: 0.7822 (tptm) cc_final: 0.7463 (tptp) REVERT: E 341 PHE cc_start: 0.3428 (OUTLIER) cc_final: 0.1790 (t80) REVERT: E 474 GLN cc_start: 0.5532 (pm20) cc_final: 0.4956 (pm20) REVERT: E 589 MET cc_start: 0.6866 (mmt) cc_final: 0.6663 (mmm) REVERT: E 785 MET cc_start: 0.1414 (tmm) cc_final: 0.0849 (tpp) REVERT: E 814 TYR cc_start: 0.3502 (OUTLIER) cc_final: 0.1352 (t80) REVERT: E 822 HIS cc_start: 0.6219 (t70) cc_final: 0.6018 (t70) REVERT: F 101 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7789 (t80) REVERT: F 153 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6165 (p90) REVERT: F 198 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6375 (mt-10) REVERT: F 286 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7402 (tm-30) REVERT: F 481 MET cc_start: 0.6776 (tpp) cc_final: 0.6037 (ttt) REVERT: G 123 SER cc_start: 0.2831 (OUTLIER) cc_final: 0.2098 (m) REVERT: G 126 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5592 (tp30) REVERT: G 239 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.4070 (tp) REVERT: H 136 GLN cc_start: 0.1913 (OUTLIER) cc_final: -0.0139 (tm-30) outliers start: 138 outliers final: 94 residues processed: 448 average time/residue: 0.2369 time to fit residues: 179.9994 Evaluate side-chains 450 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 334 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1123 TYR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 848 LEU Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 164 TYR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 743 LEU Chi-restraints excluded: chain F residue 853 LEU Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain F residue 983 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 427 optimal weight: 4.9990 chunk 475 optimal weight: 10.0000 chunk 430 optimal weight: 0.0980 chunk 357 optimal weight: 0.5980 chunk 482 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 462 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 248 optimal weight: 0.0030 chunk 228 optimal weight: 0.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 HIS ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS F 51 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 832 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.228152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.191193 restraints weight = 78402.447| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.33 r_work: 0.3808 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40974 Z= 0.140 Angle : 0.613 10.517 55500 Z= 0.311 Chirality : 0.042 0.171 6206 Planarity : 0.004 0.058 7148 Dihedral : 4.192 52.523 5496 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.49 % Favored : 93.33 % Rotamer: Outliers : 3.14 % Allowed : 25.06 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.54 (0.12), residues: 5004 helix: 1.83 (0.10), residues: 2572 sheet: 0.84 (0.42), residues: 136 loop : -1.47 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 335 TYR 0.031 0.001 TYR G 17 PHE 0.043 0.001 PHE G 268 TRP 0.022 0.001 TRP F 46 HIS 0.015 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00318 (40974) covalent geometry : angle 0.61268 (55500) hydrogen bonds : bond 0.04629 ( 1909) hydrogen bonds : angle 3.96959 ( 5532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 343 time to evaluate : 1.590 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 105 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7717 (p) REVERT: A 411 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7693 (p) REVERT: A 537 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7213 (pttm) REVERT: A 1200 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.5038 (mpt) REVERT: A 1205 LYS cc_start: 0.5487 (OUTLIER) cc_final: 0.4566 (tttm) REVERT: B 144 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7163 (ttp80) REVERT: B 153 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6236 (p90) REVERT: B 335 ARG cc_start: 0.7816 (mmt180) cc_final: 0.7221 (mpt180) REVERT: B 538 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: B 549 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6516 (tp) REVERT: B 596 ASP cc_start: 0.7508 (m-30) cc_final: 0.6563 (t0) REVERT: B 657 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6316 (tp-100) REVERT: B 804 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.3942 (pp) REVERT: B 820 GLU cc_start: 0.6264 (mp0) cc_final: 0.4219 (mm-30) REVERT: C 162 MET cc_start: 0.7773 (mmm) cc_final: 0.7567 (mmm) REVERT: C 241 MET cc_start: 0.8772 (pmm) cc_final: 0.8243 (tpp) REVERT: D 125 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5258 (tpp) REVERT: E 103 LYS cc_start: 0.5551 (OUTLIER) cc_final: 0.4761 (tptm) REVERT: E 341 PHE cc_start: 0.3588 (OUTLIER) cc_final: 0.2231 (t80) REVERT: E 474 GLN cc_start: 0.5496 (pm20) cc_final: 0.4902 (pm20) REVERT: E 589 MET cc_start: 0.6781 (mmt) cc_final: 0.6513 (mmm) REVERT: E 785 MET cc_start: 0.1100 (tmm) cc_final: 0.0599 (tpp) REVERT: E 814 TYR cc_start: 0.3511 (OUTLIER) cc_final: 0.1649 (t80) REVERT: E 822 HIS cc_start: 0.6426 (t70) cc_final: 0.6131 (t70) REVERT: F 101 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7862 (t80) REVERT: F 153 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6012 (p90) REVERT: F 198 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6574 (mt-10) REVERT: F 286 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7419 (tm-30) REVERT: F 332 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6403 (mtp85) REVERT: F 454 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8349 (tt) REVERT: F 481 MET cc_start: 0.6820 (tpp) cc_final: 0.5995 (ttt) REVERT: G 63 GLU cc_start: 0.5986 (tp30) cc_final: 0.5763 (tp30) REVERT: G 239 LEU cc_start: 0.4036 (OUTLIER) cc_final: 0.3824 (tp) REVERT: H 136 GLN cc_start: 0.1487 (OUTLIER) cc_final: 0.0090 (tm-30) outliers start: 138 outliers final: 95 residues processed: 448 average time/residue: 0.2369 time to fit residues: 180.4573 Evaluate side-chains 448 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 331 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 848 LEU Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 164 TYR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 743 LEU Chi-restraints excluded: chain F residue 853 LEU Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain F residue 983 VAL Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 54 optimal weight: 1.9990 chunk 349 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 460 optimal weight: 7.9990 chunk 432 optimal weight: 0.0060 chunk 53 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS F 51 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 657 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.228636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.195112 restraints weight = 78120.205| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.12 r_work: 0.3902 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40974 Z= 0.127 Angle : 0.613 14.948 55500 Z= 0.309 Chirality : 0.041 0.176 6206 Planarity : 0.004 0.060 7148 Dihedral : 4.148 52.055 5496 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.24 % Favored : 93.59 % Rotamer: Outliers : 2.86 % Allowed : 25.35 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.62 (0.12), residues: 5004 helix: 1.89 (0.10), residues: 2582 sheet: 0.91 (0.42), residues: 136 loop : -1.44 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 335 TYR 0.023 0.001 TYR B 53 PHE 0.045 0.001 PHE G 268 TRP 0.017 0.001 TRP F 46 HIS 0.016 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00284 (40974) covalent geometry : angle 0.61295 (55500) hydrogen bonds : bond 0.04200 ( 1909) hydrogen bonds : angle 3.91585 ( 5532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 340 time to evaluate : 1.602 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 105 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (p) REVERT: A 411 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 537 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7233 (pttm) REVERT: A 1200 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.5276 (mpt) REVERT: A 1205 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4910 (tttm) REVERT: B 144 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7450 (ttp80) REVERT: B 153 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6158 (p90) REVERT: B 369 PHE cc_start: 0.6255 (m-80) cc_final: 0.5938 (m-80) REVERT: B 538 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: B 596 ASP cc_start: 0.7307 (m-30) cc_final: 0.6588 (t0) REVERT: B 657 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6476 (tp-100) REVERT: B 820 GLU cc_start: 0.6129 (mp0) cc_final: 0.4144 (mm-30) REVERT: C 162 MET cc_start: 0.7595 (mmm) cc_final: 0.7367 (mmm) REVERT: C 241 MET cc_start: 0.8629 (pmm) cc_final: 0.8156 (tpp) REVERT: D 125 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.5014 (tpp) REVERT: E 61 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.6993 (t80) REVERT: E 103 LYS cc_start: 0.5690 (OUTLIER) cc_final: 0.4922 (tptm) REVERT: E 341 PHE cc_start: 0.3625 (OUTLIER) cc_final: 0.2216 (t80) REVERT: E 474 GLN cc_start: 0.5609 (pm20) cc_final: 0.5037 (pm20) REVERT: E 589 MET cc_start: 0.6911 (mmt) cc_final: 0.6710 (mmm) REVERT: E 785 MET cc_start: 0.1508 (tmm) cc_final: 0.1015 (tpp) REVERT: E 814 TYR cc_start: 0.3312 (OUTLIER) cc_final: 0.1251 (t80) REVERT: E 822 HIS cc_start: 0.6392 (t70) cc_final: 0.6091 (t-170) REVERT: F 101 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7723 (t80) REVERT: F 153 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6168 (p90) REVERT: F 164 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.5305 (p90) REVERT: F 198 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6268 (mt-10) REVERT: F 332 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6306 (mtp85) REVERT: F 481 MET cc_start: 0.6646 (tpp) cc_final: 0.5838 (ttt) REVERT: G 112 LEU cc_start: 0.5226 (mm) cc_final: 0.3891 (tp) REVERT: G 239 LEU cc_start: 0.4323 (OUTLIER) cc_final: 0.4101 (tp) outliers start: 126 outliers final: 88 residues processed: 431 average time/residue: 0.2352 time to fit residues: 172.2205 Evaluate side-chains 438 residues out of total 4446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 330 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 HIS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 657 GLN Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 83 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 557 THR Chi-restraints excluded: chain E residue 814 TYR Chi-restraints excluded: chain E residue 848 LEU Chi-restraints excluded: chain E residue 1069 VAL Chi-restraints excluded: chain E residue 1222 MET Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 164 TYR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain F residue 605 ILE Chi-restraints excluded: chain F residue 652 HIS Chi-restraints excluded: chain F residue 654 ASP Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 743 LEU Chi-restraints excluded: chain F residue 881 HIS Chi-restraints excluded: chain F residue 983 VAL Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 228 optimal weight: 0.9980 chunk 466 optimal weight: 0.0770 chunk 388 optimal weight: 1.9990 chunk 441 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 480 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 425 optimal weight: 8.9990 chunk 304 optimal weight: 0.0870 chunk 373 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 994 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 = 0.4717 r_free = 0.4717 target = 0.230077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.196629 restraints weight = 78835.686| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.12 r_work: 0.3869 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 40974 Z= 0.110 Angle : 0.593 13.576 55500 Z= 0.298 Chirality : 0.041 0.207 6206 Planarity : 0.004 0.059 7148 Dihedral : 4.021 52.000 5496 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.08 % Favored : 93.78 % Rotamer: Outliers : 2.32 % Allowed : 25.94 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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 aren not related in a simple way. whole: 0.76 (0.12), residues: 5004 helix: 2.02 (0.10), residues: 2570 sheet: 1.12 (0.42), residues: 132 loop : -1.38 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 845 TYR 0.022 0.001 TYR B 53 PHE 0.046 0.001 PHE G 268 TRP 0.018 0.001 TRP E 554 HIS 0.016 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00234 (40974) covalent geometry : angle 0.59262 (55500) hydrogen bonds : bond 0.03587 ( 1909) hydrogen bonds : angle 3.81805 ( 5532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11017.62 seconds wall clock time: 189 minutes 42.52 seconds (11382.52 seconds total)