Starting phenix.real_space_refine on Mon Aug 10 05:29:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr7_40721/08_2026/8sr7_40721.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr7_40721/08_2026/8sr7_40721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sr7_40721/08_2026/8sr7_40721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr7_40721/08_2026/8sr7_40721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr7_40721/08_2026/8sr7_40721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr7_40721/08_2026/8sr7_40721.map" } resolution = 1.97 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= 0.141 sd= 2.442 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 17 5.21 5 S 236 5.16 5 C 27444 2.51 5 N 7340 2.21 5 O 7748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42793 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10560 Classifications: {'peptide': 1375} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1319} Chain breaks: 3 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 17, 'GLN:plan1': 3, 'ASN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 212 Chain: "B" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10560 Classifications: {'peptide': 1375} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1319} Chain breaks: 3 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 17, 'GLN:plan1': 3, 'ASN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 212 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10560 Classifications: {'peptide': 1375} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1319} Chain breaks: 3 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 17, 'GLN:plan1': 3, 'ASN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 212 Chain: "D" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1375, 10560 Classifications: {'peptide': 1375} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1319} Chain breaks: 3 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 17, 'GLN:plan1': 3, 'ASN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 212 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 126 Unusual residues: {' MG': 5, 'AMP%rna3p': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 9} Modifications used: {'rna3p': 1} Link IDs: {None: 9} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {' MG': 4, 'AMP%rna3p': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {' MG': 4, 'AMP%rna3p': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Chain: "D" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {' MG': 4, 'AMP%rna3p': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 9.23, per 1000 atoms: 0.22 Number of scatterers: 42793 At special positions: 0 Unit cell: (159.418, 159.418, 185.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 236 16.00 P 8 15.00 Mg 17 11.99 O 7748 8.00 N 7340 7.00 C 27444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " distance=2.03 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: 3.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10352 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 36 sheets defined 59.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.545A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 203 removed outlier: 4.010A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.767A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.778A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.798A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.670A pdb=" N PHE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.801A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 4.155A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.568A pdb=" N ARG A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.539A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.964A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.904A pdb=" N ALA A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.718A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.520A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.920A pdb=" N ARG A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 799 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 859 through 866 removed outlier: 4.049A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.557A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.032A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 4.021A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.815A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.715A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.679A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.839A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 4.181A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1169 removed outlier: 3.593A pdb=" N ALA A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 4.192A pdb=" N LYS A1272 " --> pdb=" O ASP A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1391 removed outlier: 3.855A pdb=" N GLY A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1413 removed outlier: 3.720A pdb=" N ASP A1407 " --> pdb=" O ALA A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.720A pdb=" N ARG A1452 " --> pdb=" O ARG A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1491 Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.545A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 203 removed outlier: 4.010A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 287 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.768A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.778A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.798A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.670A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.801A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 4.155A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.568A pdb=" N ARG B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.538A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.964A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.904A pdb=" N ALA B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.718A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.520A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.920A pdb=" N ARG B 792 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 799 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 Processing helix chain 'B' and resid 859 through 866 removed outlier: 4.049A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.557A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.032A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 4.021A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.815A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.715A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.679A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.839A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 4.181A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1169 removed outlier: 3.593A pdb=" N ALA B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B1169 " --> pdb=" O ASP B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1206 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1269 through 1273 removed outlier: 4.192A pdb=" N LYS B1272 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1378 through 1391 removed outlier: 3.856A pdb=" N GLY B1384 " --> pdb=" O ALA B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1413 removed outlier: 3.720A pdb=" N ASP B1407 " --> pdb=" O ALA B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1452 removed outlier: 3.720A pdb=" N ARG B1452 " --> pdb=" O ARG B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1491 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.545A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 203 removed outlier: 4.010A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 287 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.767A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.778A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 407 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.798A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.670A pdb=" N PHE C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.801A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 4.155A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 3.568A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.539A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.964A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 581 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.904A pdb=" N ALA C 599 " --> pdb=" O ARG C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.718A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.520A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.920A pdb=" N ARG C 792 " --> pdb=" O ALA C 788 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 799 " --> pdb=" O PHE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 Processing helix chain 'C' and resid 859 through 866 removed outlier: 4.049A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.557A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.032A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 4.021A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.815A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.715A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1010 through 1012 No H-bonds generated for 'chain 'C' and resid 1010 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.679A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.839A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 4.181A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1169 removed outlier: 3.593A pdb=" N ALA C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C1169 " --> pdb=" O ASP C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1206 Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1269 through 1273 removed outlier: 4.192A pdb=" N LYS C1272 " --> pdb=" O ASP C1269 " (cutoff:3.500A) Processing helix chain 'C' and resid 1378 through 1391 removed outlier: 3.855A pdb=" N GLY C1384 " --> pdb=" O ALA C1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 1402 through 1413 removed outlier: 3.720A pdb=" N ASP C1407 " --> pdb=" O ALA C1403 " (cutoff:3.500A) Processing helix chain 'C' and resid 1447 through 1452 removed outlier: 3.720A pdb=" N ARG C1452 " --> pdb=" O ARG C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1491 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.545A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 203 removed outlier: 4.010A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 287 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.767A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.778A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.798A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.670A pdb=" N PHE D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.801A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 4.155A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 removed outlier: 3.568A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.539A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.964A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 581 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.904A pdb=" N ALA D 599 " --> pdb=" O ARG D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.718A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.520A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.920A pdb=" N ARG D 792 " --> pdb=" O ALA D 788 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 799 " --> pdb=" O PHE D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 Processing helix chain 'D' and resid 859 through 866 removed outlier: 4.049A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.557A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.032A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 4.021A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.815A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.715A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.679A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.839A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 4.181A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1169 removed outlier: 3.593A pdb=" N ALA D1168 " --> pdb=" O LEU D1164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR D1169 " --> pdb=" O ASP D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1269 through 1273 removed outlier: 4.192A pdb=" N LYS D1272 " --> pdb=" O ASP D1269 " (cutoff:3.500A) Processing helix chain 'D' and resid 1378 through 1391 removed outlier: 3.855A pdb=" N GLY D1384 " --> pdb=" O ALA D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1402 through 1413 removed outlier: 3.720A pdb=" N ASP D1407 " --> pdb=" O ALA D1403 " (cutoff:3.500A) Processing helix chain 'D' and resid 1447 through 1452 removed outlier: 3.720A pdb=" N ARG D1452 " --> pdb=" O ARG D1448 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1491 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.550A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 6.064A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TYR A1253 " --> pdb=" O ARG A1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA6, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 4.163A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.533A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.593A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP A1336 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.593A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A1353 " --> pdb=" O MET A1468 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET A1468 " --> pdb=" O LEU A1353 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A1355 " --> pdb=" O TRP A1466 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP A1466 " --> pdb=" O PHE A1355 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A1357 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A1464 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A1359 " --> pdb=" O GLU A1462 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.550A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 6.064A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG B1317 " --> pdb=" O VAL B1251 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TYR B1253 " --> pdb=" O ARG B1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AB6, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 4.163A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.533A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.592A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 17.592A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B1353 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET B1468 " --> pdb=" O LEU B1353 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B1355 " --> pdb=" O TRP B1466 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B1466 " --> pdb=" O PHE B1355 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B1357 " --> pdb=" O ALA B1464 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B1464 " --> pdb=" O ALA B1357 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B1359 " --> pdb=" O GLU B1462 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC1, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.550A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 6.064A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG C1317 " --> pdb=" O VAL C1251 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TYR C1253 " --> pdb=" O ARG C1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AC6, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 4.163A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.533A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.593A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 17.593A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU C1353 " --> pdb=" O MET C1468 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET C1468 " --> pdb=" O LEU C1353 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE C1355 " --> pdb=" O TRP C1466 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP C1466 " --> pdb=" O PHE C1355 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C1357 " --> pdb=" O ALA C1464 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA C1464 " --> pdb=" O ALA C1357 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN C1359 " --> pdb=" O GLU C1462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD3, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.550A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 6.064A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TYR D1253 " --> pdb=" O ARG D1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD6, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 4.163A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.532A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.593A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 17.593A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU D1353 " --> pdb=" O MET D1468 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N MET D1468 " --> pdb=" O LEU D1353 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE D1355 " --> pdb=" O TRP D1466 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP D1466 " --> pdb=" O PHE D1355 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA D1357 " --> pdb=" O ALA D1464 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA D1464 " --> pdb=" O ALA D1357 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN D1359 " --> pdb=" O GLU D1462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2384 hydrogen bonds defined for protein. 6984 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: 12.08 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6964 1.31 - 1.44: 11680 1.44 - 1.56: 24648 1.56 - 1.69: 20 1.69 - 1.82: 420 Bond restraints: 43732 Sorted by residual: bond pdb=" C2 RP5 D6003 " pdb=" C3 RP5 D6003 " ideal model delta sigma weight residual 1.525 1.247 0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C2 RP5 C1501 " pdb=" C3 RP5 C1501 " ideal model delta sigma weight residual 1.525 1.247 0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C2 RP5 B1501 " pdb=" C3 RP5 B1501 " ideal model delta sigma weight residual 1.525 1.247 0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C2 RP5 A1501 " pdb=" C3 RP5 A1501 " ideal model delta sigma weight residual 1.525 1.247 0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C1 RP5 B1501 " pdb=" O1 RP5 B1501 " ideal model delta sigma weight residual 1.404 1.268 0.136 2.00e-02 2.50e+03 4.59e+01 ... (remaining 43727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 52635 2.27 - 4.55: 5729 4.55 - 6.82: 917 6.82 - 9.10: 163 9.10 - 11.37: 16 Bond angle restraints: 59460 Sorted by residual: angle pdb=" N PRO D 244 " pdb=" CA PRO D 244 " pdb=" C PRO D 244 " ideal model delta sigma weight residual 110.70 119.46 -8.76 1.22e+00 6.72e-01 5.16e+01 angle pdb=" N PRO A 244 " pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 110.70 119.43 -8.73 1.22e+00 6.72e-01 5.12e+01 angle pdb=" N PRO B 244 " pdb=" CA PRO B 244 " pdb=" C PRO B 244 " ideal model delta sigma weight residual 110.70 119.43 -8.73 1.22e+00 6.72e-01 5.12e+01 angle pdb=" N PRO C 244 " pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 110.70 119.43 -8.73 1.22e+00 6.72e-01 5.12e+01 angle pdb=" CA ASP D1459 " pdb=" C ASP D1459 " pdb=" N ASP D1460 " ideal model delta sigma weight residual 119.63 114.02 5.61 8.10e-01 1.52e+00 4.80e+01 ... (remaining 59455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.72: 25704 26.72 - 53.44: 788 53.44 - 80.15: 100 80.15 - 106.87: 20 106.87 - 133.59: 4 Dihedral angle restraints: 26616 sinusoidal: 10628 harmonic: 15988 Sorted by residual: dihedral pdb=" C2' AMP D6004 " pdb=" C1' AMP D6004 " pdb=" N9 AMP D6004 " pdb=" C4 AMP D6004 " ideal model delta sinusoidal sigma weight residual 91.55 -42.04 133.59 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C2' AMP A1502 " pdb=" C1' AMP A1502 " pdb=" N9 AMP A1502 " pdb=" C4 AMP A1502 " ideal model delta sinusoidal sigma weight residual 91.55 -42.04 133.59 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C2' AMP C1502 " pdb=" C1' AMP C1502 " pdb=" N9 AMP C1502 " pdb=" C4 AMP C1502 " ideal model delta sinusoidal sigma weight residual 91.55 -42.04 133.59 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 26613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5671 0.106 - 0.213: 894 0.213 - 0.319: 123 0.319 - 0.425: 28 0.425 - 0.532: 12 Chirality restraints: 6728 Sorted by residual: chirality pdb=" CA GLN D1261 " pdb=" N GLN D1261 " pdb=" C GLN D1261 " pdb=" CB GLN D1261 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA GLN A1261 " pdb=" N GLN A1261 " pdb=" C GLN A1261 " pdb=" CB GLN A1261 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA GLN B1261 " pdb=" N GLN B1261 " pdb=" C GLN B1261 " pdb=" CB GLN B1261 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.06e+00 ... (remaining 6725 not shown) Planarity restraints: 7572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1151 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C ASP A1151 " -0.082 2.00e-02 2.50e+03 pdb=" O ASP A1151 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN A1152 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1151 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C ASP B1151 " -0.082 2.00e-02 2.50e+03 pdb=" O ASP B1151 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN B1152 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C1151 " -0.023 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C ASP C1151 " 0.082 2.00e-02 2.50e+03 pdb=" O ASP C1151 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN C1152 " -0.028 2.00e-02 2.50e+03 ... (remaining 7569 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 764 2.68 - 3.24: 37562 3.24 - 3.79: 67054 3.79 - 4.35: 91539 4.35 - 4.90: 152064 Nonbonded interactions: 348983 Sorted by model distance: nonbonded pdb=" O1X RP5 A1501 " pdb="MG MG A1505 " model vdw 2.129 2.170 nonbonded pdb=" O1X RP5 C1501 " pdb="MG MG C1505 " model vdw 2.129 2.170 nonbonded pdb=" O1X RP5 D6003 " pdb="MG MG D6007 " model vdw 2.129 2.170 nonbonded pdb=" O1X RP5 B1501 " pdb="MG MG B1505 " model vdw 2.129 2.170 nonbonded pdb=" OE1 GLU C1390 " pdb="MG MG C1505 " model vdw 2.131 2.170 ... (remaining 348978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 51 through 1494 or resid 1505 through 1506 or resid 1509)) \ selection = (chain 'B' and (resid 51 through 1494 or resid 1505 through 1506 or resid 1509)) \ selection = (chain 'C' and (resid 51 through 1494 or resid 1505 through 1506 or resid 1509)) \ selection = (chain 'D' and (resid 51 through 1494 or resid 6005 through 6006 or resid 6009)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 42.770 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.011 0.278 43736 Z= 0.658 Angle : 1.509 11.369 59468 Z= 0.991 Chirality : 0.083 0.532 6728 Planarity : 0.010 0.047 7572 Dihedral : 13.586 133.592 16252 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.11), residues: 5468 helix: 0.98 (0.09), residues: 2964 sheet: -0.87 (0.21), residues: 464 loop : -0.27 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 655 TYR 0.037 0.005 TYR A 466 PHE 0.054 0.005 PHE C 941 TRP 0.023 0.003 TRP B 726 HIS 0.021 0.002 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.66 (43732) covalent geometry : angle 1.50921 / 0.99 (59460) SS BOND : bond 0.00465 / 0.23 ( 4) SS BOND : angle 1.49826 / 0.88 ( 8) hydrogen bonds : bond 0.16562 / 11.04 ( 2372) hydrogen bonds : angle 7.10316 / 5.16 ( 6984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 957 time to evaluate : 1.531 Fit side-chains REVERT: A 55 LYS cc_start: 0.6723 (mttt) cc_final: 0.5964 (mptt) REVERT: A 60 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6142 (mt-10) REVERT: A 74 ASP cc_start: 0.6127 (t0) cc_final: 0.5817 (t0) REVERT: A 80 HIS cc_start: 0.6651 (m90) cc_final: 0.6151 (m90) REVERT: A 118 ASP cc_start: 0.6400 (t0) cc_final: 0.6174 (t0) REVERT: A 129 MET cc_start: 0.7468 (mmp) cc_final: 0.7255 (mmp) REVERT: A 166 LYS cc_start: 0.6503 (tttm) cc_final: 0.5608 (mptt) REVERT: A 173 GLN cc_start: 0.6355 (pt0) cc_final: 0.5840 (tm-30) REVERT: A 190 LYS cc_start: 0.6613 (ttpt) cc_final: 0.6226 (ttmm) REVERT: A 197 GLU cc_start: 0.5953 (tt0) cc_final: 0.5725 (tt0) REVERT: A 224 ASP cc_start: 0.6691 (m-30) cc_final: 0.5973 (t0) REVERT: A 236 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5512 (mm-30) REVERT: A 273 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6732 (tmtm) REVERT: A 371 ASP cc_start: 0.7156 (t70) cc_final: 0.6642 (m-30) REVERT: A 381 ASN cc_start: 0.7297 (m-40) cc_final: 0.6921 (m110) REVERT: A 395 GLU cc_start: 0.5971 (mm-30) cc_final: 0.5404 (mp0) REVERT: A 402 LYS cc_start: 0.6305 (mtmt) cc_final: 0.5726 (ttpt) REVERT: A 407 SER cc_start: 0.6858 (t) cc_final: 0.6510 (p) REVERT: A 413 ASN cc_start: 0.6409 (m-40) cc_final: 0.6124 (m-40) REVERT: A 428 LYS cc_start: 0.5556 (mttt) cc_final: 0.5309 (mtpt) REVERT: A 449 ASP cc_start: 0.6333 (t0) cc_final: 0.6115 (t0) REVERT: A 464 GLU cc_start: 0.5760 (mt-10) cc_final: 0.5557 (mt-10) REVERT: A 474 TYR cc_start: 0.6721 (p90) cc_final: 0.6431 (p90) REVERT: A 498 LEU cc_start: 0.6766 (mt) cc_final: 0.6489 (mp) REVERT: A 506 ARG cc_start: 0.6249 (ttt-90) cc_final: 0.5308 (tmm160) REVERT: A 516 GLN cc_start: 0.5595 (tt0) cc_final: 0.4782 (pp30) REVERT: A 614 ARG cc_start: 0.5861 (mtm180) cc_final: 0.5600 (mtm-85) REVERT: A 622 ILE cc_start: 0.6659 (mt) cc_final: 0.6393 (mm) REVERT: A 625 GLN cc_start: 0.6470 (mm-40) cc_final: 0.6227 (mm-40) REVERT: A 638 GLU cc_start: 0.5709 (mt-10) cc_final: 0.5227 (mt-10) REVERT: A 654 GLU cc_start: 0.5191 (tp30) cc_final: 0.4977 (tp30) REVERT: A 657 LYS cc_start: 0.5762 (ttpp) cc_final: 0.5209 (ttpm) REVERT: A 663 LYS cc_start: 0.6205 (tptm) cc_final: 0.5788 (mtpt) REVERT: A 666 GLU cc_start: 0.6039 (tt0) cc_final: 0.5629 (tt0) REVERT: A 667 GLU cc_start: 0.5604 (mt-10) cc_final: 0.5239 (mt-10) REVERT: A 686 GLU cc_start: 0.5700 (mm-30) cc_final: 0.4831 (mm-30) REVERT: A 694 MET cc_start: 0.4612 (mtm) cc_final: 0.4177 (pmm) REVERT: A 699 ASN cc_start: 0.5860 (p0) cc_final: 0.5597 (p0) REVERT: A 729 HIS cc_start: 0.5699 (m90) cc_final: 0.5386 (m90) REVERT: A 805 ARG cc_start: 0.6629 (mtt180) cc_final: 0.6392 (mtm180) REVERT: A 915 MET cc_start: 0.7369 (mtm) cc_final: 0.7070 (mtt) REVERT: A 916 ARG cc_start: 0.6420 (tpm170) cc_final: 0.6136 (tpm170) REVERT: A 922 LYS cc_start: 0.6430 (ptpp) cc_final: 0.5911 (ptpp) REVERT: A 932 MET cc_start: 0.5948 (mmt) cc_final: 0.5372 (mmm) REVERT: A 936 LYS cc_start: 0.5729 (mtmt) cc_final: 0.5368 (mttp) REVERT: A 964 GLU cc_start: 0.7146 (tt0) cc_final: 0.6223 (pt0) REVERT: A 969 ARG cc_start: 0.6627 (mtm110) cc_final: 0.5831 (mtm-85) REVERT: A 989 ASP cc_start: 0.6385 (m-30) cc_final: 0.5316 (p0) REVERT: A 1042 MET cc_start: 0.6328 (mtm) cc_final: 0.5220 (mmm) REVERT: A 1043 LYS cc_start: 0.6320 (mttp) cc_final: 0.6064 (mttt) REVERT: A 1107 ARG cc_start: 0.4922 (ptp-110) cc_final: 0.4626 (ptp90) REVERT: A 1118 ASP cc_start: 0.5952 (m-30) cc_final: 0.5433 (m-30) REVERT: A 1119 LYS cc_start: 0.6574 (tttm) cc_final: 0.5968 (ttpp) REVERT: A 1122 ARG cc_start: 0.5974 (mtm-85) cc_final: 0.5339 (mtm-85) REVERT: A 1124 TRP cc_start: 0.6160 (t60) cc_final: 0.5832 (t60) REVERT: A 1128 ARG cc_start: 0.5352 (ttp80) cc_final: 0.4599 (tpt-90) REVERT: A 1129 GLN cc_start: 0.5180 (mm110) cc_final: 0.4943 (mm-40) REVERT: A 1131 MET cc_start: 0.5594 (mmp) cc_final: 0.5228 (mtm) REVERT: A 1133 GLU cc_start: 0.6269 (mm-30) cc_final: 0.6015 (mp0) REVERT: A 1154 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6283 (mt) REVERT: A 1156 HIS cc_start: 0.4861 (m90) cc_final: 0.4586 (m-70) REVERT: A 1199 ARG cc_start: 0.6818 (tpp-160) cc_final: 0.6331 (tpt170) REVERT: A 1200 LEU cc_start: 0.6779 (tp) cc_final: 0.6562 (tp) REVERT: A 1222 GLU cc_start: 0.7051 (tt0) cc_final: 0.6439 (tp30) REVERT: A 1346 GLU cc_start: 0.7805 (tt0) cc_final: 0.7392 (tt0) REVERT: A 1394 MET cc_start: 0.6920 (mmm) cc_final: 0.6655 (mtp) REVERT: A 1459 ASP cc_start: 0.6237 (t0) cc_final: 0.5880 (m-30) REVERT: B 55 LYS cc_start: 0.6671 (mttt) cc_final: 0.5934 (mptt) REVERT: B 74 ASP cc_start: 0.6129 (t0) cc_final: 0.5824 (t0) REVERT: B 80 HIS cc_start: 0.6648 (m90) cc_final: 0.6152 (m90) REVERT: B 118 ASP cc_start: 0.6418 (t0) cc_final: 0.6192 (t0) REVERT: B 129 MET cc_start: 0.7471 (mmp) cc_final: 0.7266 (mmp) REVERT: B 166 LYS cc_start: 0.6527 (tttm) cc_final: 0.5623 (mptt) REVERT: B 173 GLN cc_start: 0.6368 (pt0) cc_final: 0.5846 (tm-30) REVERT: B 190 LYS cc_start: 0.6606 (ttpt) cc_final: 0.6221 (ttmm) REVERT: B 197 GLU cc_start: 0.5963 (tt0) cc_final: 0.5734 (tt0) REVERT: B 236 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5489 (mm-30) REVERT: B 273 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6724 (tmtm) REVERT: B 371 ASP cc_start: 0.7136 (t70) cc_final: 0.6632 (m-30) REVERT: B 381 ASN cc_start: 0.7273 (m-40) cc_final: 0.6918 (m110) REVERT: B 395 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5408 (mp0) REVERT: B 402 LYS cc_start: 0.6344 (mtmt) cc_final: 0.5637 (ttpt) REVERT: B 407 SER cc_start: 0.6877 (t) cc_final: 0.6515 (p) REVERT: B 413 ASN cc_start: 0.6396 (m-40) cc_final: 0.6111 (m-40) REVERT: B 428 LYS cc_start: 0.5549 (mttt) cc_final: 0.5315 (mtpt) REVERT: B 449 ASP cc_start: 0.6332 (t0) cc_final: 0.6107 (t0) REVERT: B 464 GLU cc_start: 0.5760 (mt-10) cc_final: 0.5555 (mt-10) REVERT: B 474 TYR cc_start: 0.6736 (p90) cc_final: 0.6451 (p90) REVERT: B 498 LEU cc_start: 0.6763 (mt) cc_final: 0.6484 (mp) REVERT: B 506 ARG cc_start: 0.6246 (ttt-90) cc_final: 0.5313 (tmm160) REVERT: B 516 GLN cc_start: 0.5550 (tt0) cc_final: 0.4733 (pp30) REVERT: B 614 ARG cc_start: 0.5860 (mtm180) cc_final: 0.5592 (mtm-85) REVERT: B 622 ILE cc_start: 0.6703 (mt) cc_final: 0.6440 (mm) REVERT: B 625 GLN cc_start: 0.6474 (mm-40) cc_final: 0.6228 (mm-40) REVERT: B 638 GLU cc_start: 0.5690 (mt-10) cc_final: 0.5204 (mt-10) REVERT: B 653 GLU cc_start: 0.4598 (mt-10) cc_final: 0.4380 (pm20) REVERT: B 654 GLU cc_start: 0.5202 (tp30) cc_final: 0.4983 (tp30) REVERT: B 657 LYS cc_start: 0.5759 (ttpp) cc_final: 0.5205 (ttpm) REVERT: B 663 LYS cc_start: 0.6213 (tptm) cc_final: 0.5707 (ttmt) REVERT: B 666 GLU cc_start: 0.6034 (tt0) cc_final: 0.5634 (tt0) REVERT: B 667 GLU cc_start: 0.5599 (mt-10) cc_final: 0.5221 (mt-10) REVERT: B 686 GLU cc_start: 0.5636 (mm-30) cc_final: 0.4775 (mm-30) REVERT: B 694 MET cc_start: 0.4614 (mtm) cc_final: 0.4190 (pmm) REVERT: B 699 ASN cc_start: 0.5820 (p0) cc_final: 0.5556 (p0) REVERT: B 729 HIS cc_start: 0.5711 (m90) cc_final: 0.5394 (m90) REVERT: B 805 ARG cc_start: 0.6629 (mtt180) cc_final: 0.6394 (mtm180) REVERT: B 915 MET cc_start: 0.7327 (mtm) cc_final: 0.7036 (mtt) REVERT: B 916 ARG cc_start: 0.6474 (tpm170) cc_final: 0.6232 (tpm170) REVERT: B 922 LYS cc_start: 0.6460 (ptpp) cc_final: 0.5942 (ptpp) REVERT: B 932 MET cc_start: 0.5941 (mmt) cc_final: 0.5326 (mmm) REVERT: B 935 MET cc_start: 0.6580 (mmm) cc_final: 0.5536 (mmm) REVERT: B 936 LYS cc_start: 0.5690 (mtmt) cc_final: 0.5336 (mttp) REVERT: B 964 GLU cc_start: 0.7152 (tt0) cc_final: 0.6231 (pt0) REVERT: B 969 ARG cc_start: 0.6633 (mtm110) cc_final: 0.5822 (mtm-85) REVERT: B 989 ASP cc_start: 0.6332 (m-30) cc_final: 0.5267 (p0) REVERT: B 1042 MET cc_start: 0.6402 (mtm) cc_final: 0.5300 (mmm) REVERT: B 1107 ARG cc_start: 0.4916 (ptp-110) cc_final: 0.4634 (ptp90) REVERT: B 1118 ASP cc_start: 0.5951 (m-30) cc_final: 0.5430 (m-30) REVERT: B 1119 LYS cc_start: 0.6583 (tttm) cc_final: 0.5970 (ttpp) REVERT: B 1122 ARG cc_start: 0.5950 (mtm-85) cc_final: 0.5303 (mtm-85) REVERT: B 1124 TRP cc_start: 0.6231 (t60) cc_final: 0.5909 (t60) REVERT: B 1128 ARG cc_start: 0.5355 (ttp80) cc_final: 0.4612 (tpt-90) REVERT: B 1131 MET cc_start: 0.5615 (mmp) cc_final: 0.5320 (mtm) REVERT: B 1133 GLU cc_start: 0.6290 (mm-30) cc_final: 0.6021 (mp0) REVERT: B 1154 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6264 (mt) REVERT: B 1156 HIS cc_start: 0.4867 (m90) cc_final: 0.4592 (m-70) REVERT: B 1199 ARG cc_start: 0.6798 (tpp-160) cc_final: 0.6320 (tpt170) REVERT: B 1200 LEU cc_start: 0.6772 (tp) cc_final: 0.6561 (tp) REVERT: B 1222 GLU cc_start: 0.7032 (tt0) cc_final: 0.6425 (tp30) REVERT: B 1394 MET cc_start: 0.6912 (mmm) cc_final: 0.6662 (mtp) REVERT: B 1459 ASP cc_start: 0.6228 (t0) cc_final: 0.5872 (m-30) REVERT: C 55 LYS cc_start: 0.6671 (mttt) cc_final: 0.5939 (mptt) REVERT: C 74 ASP cc_start: 0.6129 (t0) cc_final: 0.5822 (t0) REVERT: C 80 HIS cc_start: 0.6647 (m90) cc_final: 0.6151 (m90) REVERT: C 118 ASP cc_start: 0.6400 (t0) cc_final: 0.6139 (t0) REVERT: C 129 MET cc_start: 0.7471 (mmp) cc_final: 0.7265 (mmp) REVERT: C 166 LYS cc_start: 0.6559 (tttm) cc_final: 0.5689 (mptt) REVERT: C 173 GLN cc_start: 0.6366 (pt0) cc_final: 0.5845 (tm-30) REVERT: C 190 LYS cc_start: 0.6605 (ttpt) cc_final: 0.6221 (ttmm) REVERT: C 197 GLU cc_start: 0.5961 (tt0) cc_final: 0.5731 (tt0) REVERT: C 236 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5489 (mm-30) REVERT: C 273 LYS cc_start: 0.7053 (mtpt) cc_final: 0.6725 (tmtm) REVERT: C 371 ASP cc_start: 0.7135 (t70) cc_final: 0.6632 (m-30) REVERT: C 381 ASN cc_start: 0.7271 (m-40) cc_final: 0.6916 (m110) REVERT: C 395 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5407 (mp0) REVERT: C 402 LYS cc_start: 0.6344 (mtmt) cc_final: 0.5638 (ttpt) REVERT: C 407 SER cc_start: 0.6881 (t) cc_final: 0.6516 (p) REVERT: C 413 ASN cc_start: 0.6414 (m-40) cc_final: 0.6137 (m-40) REVERT: C 428 LYS cc_start: 0.5545 (mttt) cc_final: 0.5312 (mtpt) REVERT: C 449 ASP cc_start: 0.6332 (t0) cc_final: 0.6108 (t0) REVERT: C 464 GLU cc_start: 0.5759 (mt-10) cc_final: 0.5555 (mt-10) REVERT: C 474 TYR cc_start: 0.6761 (p90) cc_final: 0.6476 (p90) REVERT: C 498 LEU cc_start: 0.6761 (mt) cc_final: 0.6484 (mp) REVERT: C 506 ARG cc_start: 0.6252 (ttt-90) cc_final: 0.5309 (tmm160) REVERT: C 516 GLN cc_start: 0.5593 (tt0) cc_final: 0.4789 (pp30) REVERT: C 614 ARG cc_start: 0.5860 (mtm180) cc_final: 0.5592 (mtm-85) REVERT: C 622 ILE cc_start: 0.6703 (mt) cc_final: 0.6439 (mm) REVERT: C 625 GLN cc_start: 0.6473 (mm-40) cc_final: 0.6225 (mm-40) REVERT: C 638 GLU cc_start: 0.5689 (mt-10) cc_final: 0.5205 (mt-10) REVERT: C 653 GLU cc_start: 0.4597 (mt-10) cc_final: 0.4379 (pm20) REVERT: C 654 GLU cc_start: 0.5202 (tp30) cc_final: 0.4979 (tp30) REVERT: C 657 LYS cc_start: 0.5759 (ttpp) cc_final: 0.5202 (ttpm) REVERT: C 663 LYS cc_start: 0.6210 (tptm) cc_final: 0.5705 (ttmt) REVERT: C 666 GLU cc_start: 0.6052 (tt0) cc_final: 0.5648 (tt0) REVERT: C 667 GLU cc_start: 0.5594 (mt-10) cc_final: 0.5217 (mt-10) REVERT: C 686 GLU cc_start: 0.5637 (mm-30) cc_final: 0.4775 (mm-30) REVERT: C 694 MET cc_start: 0.4611 (mtm) cc_final: 0.4186 (pmm) REVERT: C 699 ASN cc_start: 0.5818 (p0) cc_final: 0.5554 (p0) REVERT: C 729 HIS cc_start: 0.5711 (m90) cc_final: 0.5394 (m90) REVERT: C 805 ARG cc_start: 0.6624 (mtt180) cc_final: 0.6389 (mtm180) REVERT: C 915 MET cc_start: 0.7327 (mtm) cc_final: 0.7037 (mtt) REVERT: C 916 ARG cc_start: 0.6474 (tpm170) cc_final: 0.6232 (tpm170) REVERT: C 922 LYS cc_start: 0.6461 (ptpp) cc_final: 0.5943 (ptpp) REVERT: C 932 MET cc_start: 0.5939 (mmt) cc_final: 0.5325 (mmm) REVERT: C 935 MET cc_start: 0.6537 (mmm) cc_final: 0.5504 (mmm) REVERT: C 936 LYS cc_start: 0.5688 (mtmt) cc_final: 0.5334 (mttp) REVERT: C 964 GLU cc_start: 0.7151 (tt0) cc_final: 0.6236 (pt0) REVERT: C 969 ARG cc_start: 0.6643 (mtm110) cc_final: 0.5832 (mtm-85) REVERT: C 989 ASP cc_start: 0.6333 (m-30) cc_final: 0.5266 (p0) REVERT: C 1042 MET cc_start: 0.6404 (mtm) cc_final: 0.5301 (mmm) REVERT: C 1107 ARG cc_start: 0.4910 (ptp-110) cc_final: 0.4630 (ptp90) REVERT: C 1118 ASP cc_start: 0.5951 (m-30) cc_final: 0.5430 (m-30) REVERT: C 1119 LYS cc_start: 0.6553 (tttm) cc_final: 0.5944 (ttpp) REVERT: C 1122 ARG cc_start: 0.5951 (mtm-85) cc_final: 0.5304 (mtm-85) REVERT: C 1124 TRP cc_start: 0.6233 (t60) cc_final: 0.5910 (t60) REVERT: C 1128 ARG cc_start: 0.5356 (ttp80) cc_final: 0.4613 (tpt-90) REVERT: C 1131 MET cc_start: 0.5615 (mmp) cc_final: 0.5321 (mtm) REVERT: C 1133 GLU cc_start: 0.6292 (mm-30) cc_final: 0.6022 (mp0) REVERT: C 1154 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6276 (mt) REVERT: C 1156 HIS cc_start: 0.4867 (m90) cc_final: 0.4597 (m-70) REVERT: C 1199 ARG cc_start: 0.6803 (tpp-160) cc_final: 0.6321 (tpt170) REVERT: C 1200 LEU cc_start: 0.6777 (tp) cc_final: 0.6541 (tp) REVERT: C 1222 GLU cc_start: 0.7030 (tt0) cc_final: 0.6424 (tp30) REVERT: C 1394 MET cc_start: 0.6913 (mmm) cc_final: 0.6663 (mtp) REVERT: C 1459 ASP cc_start: 0.6231 (t0) cc_final: 0.5874 (m-30) REVERT: D 55 LYS cc_start: 0.6670 (mttt) cc_final: 0.5938 (mptt) REVERT: D 74 ASP cc_start: 0.6119 (t0) cc_final: 0.5812 (t0) REVERT: D 80 HIS cc_start: 0.6647 (m90) cc_final: 0.6152 (m90) REVERT: D 118 ASP cc_start: 0.6400 (t0) cc_final: 0.6173 (t0) REVERT: D 129 MET cc_start: 0.7473 (mmp) cc_final: 0.7267 (mmp) REVERT: D 166 LYS cc_start: 0.6557 (tttm) cc_final: 0.5700 (mptt) REVERT: D 173 GLN cc_start: 0.6365 (pt0) cc_final: 0.5845 (tm-30) REVERT: D 190 LYS cc_start: 0.6606 (ttpt) cc_final: 0.6221 (ttmm) REVERT: D 197 GLU cc_start: 0.5957 (tt0) cc_final: 0.5728 (tt0) REVERT: D 236 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5488 (mm-30) REVERT: D 273 LYS cc_start: 0.7052 (mtpt) cc_final: 0.6725 (tmtm) REVERT: D 371 ASP cc_start: 0.7134 (t70) cc_final: 0.6630 (m-30) REVERT: D 381 ASN cc_start: 0.7268 (m-40) cc_final: 0.6917 (m110) REVERT: D 395 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5404 (mp0) REVERT: D 402 LYS cc_start: 0.6345 (mtmt) cc_final: 0.5637 (ttpt) REVERT: D 407 SER cc_start: 0.6880 (t) cc_final: 0.6515 (p) REVERT: D 413 ASN cc_start: 0.6410 (m-40) cc_final: 0.6135 (m-40) REVERT: D 428 LYS cc_start: 0.5572 (mttt) cc_final: 0.5326 (mtpt) REVERT: D 449 ASP cc_start: 0.6336 (t0) cc_final: 0.6107 (t0) REVERT: D 464 GLU cc_start: 0.5758 (mt-10) cc_final: 0.5555 (mt-10) REVERT: D 474 TYR cc_start: 0.6727 (p90) cc_final: 0.6439 (p90) REVERT: D 498 LEU cc_start: 0.6759 (mt) cc_final: 0.6482 (mp) REVERT: D 506 ARG cc_start: 0.6249 (ttt-90) cc_final: 0.5309 (tmm160) REVERT: D 516 GLN cc_start: 0.5592 (tt0) cc_final: 0.4779 (pp30) REVERT: D 614 ARG cc_start: 0.5860 (mtm180) cc_final: 0.5593 (mtm-85) REVERT: D 622 ILE cc_start: 0.6700 (mt) cc_final: 0.6437 (mm) REVERT: D 625 GLN cc_start: 0.6471 (mm-40) cc_final: 0.6228 (mm-40) REVERT: D 638 GLU cc_start: 0.5690 (mt-10) cc_final: 0.5206 (mt-10) REVERT: D 653 GLU cc_start: 0.4603 (mt-10) cc_final: 0.4385 (pm20) REVERT: D 654 GLU cc_start: 0.5202 (tp30) cc_final: 0.4987 (tp30) REVERT: D 657 LYS cc_start: 0.5758 (ttpp) cc_final: 0.5206 (ttpm) REVERT: D 663 LYS cc_start: 0.6225 (tptm) cc_final: 0.5704 (ttmt) REVERT: D 666 GLU cc_start: 0.6041 (tt0) cc_final: 0.5634 (tt0) REVERT: D 667 GLU cc_start: 0.5593 (mt-10) cc_final: 0.5216 (mt-10) REVERT: D 686 GLU cc_start: 0.5635 (mm-30) cc_final: 0.4775 (mm-30) REVERT: D 694 MET cc_start: 0.4611 (mtm) cc_final: 0.4186 (pmm) REVERT: D 699 ASN cc_start: 0.5818 (p0) cc_final: 0.5554 (p0) REVERT: D 729 HIS cc_start: 0.5707 (m90) cc_final: 0.5391 (m90) REVERT: D 805 ARG cc_start: 0.6623 (mtt180) cc_final: 0.6388 (mtm180) REVERT: D 915 MET cc_start: 0.7326 (mtm) cc_final: 0.7037 (mtt) REVERT: D 916 ARG cc_start: 0.6474 (tpm170) cc_final: 0.6190 (tpm170) REVERT: D 922 LYS cc_start: 0.6459 (ptpp) cc_final: 0.5942 (ptpp) REVERT: D 932 MET cc_start: 0.5941 (mmt) cc_final: 0.5324 (mmm) REVERT: D 935 MET cc_start: 0.6538 (mmm) cc_final: 0.5506 (mmm) REVERT: D 936 LYS cc_start: 0.5690 (mtmt) cc_final: 0.5337 (mttp) REVERT: D 964 GLU cc_start: 0.7148 (tt0) cc_final: 0.6226 (pt0) REVERT: D 969 ARG cc_start: 0.6645 (mtm110) cc_final: 0.5831 (mtm-85) REVERT: D 989 ASP cc_start: 0.6333 (m-30) cc_final: 0.5267 (p0) REVERT: D 1042 MET cc_start: 0.6403 (mtm) cc_final: 0.5301 (mmm) REVERT: D 1107 ARG cc_start: 0.4907 (ptp-110) cc_final: 0.4627 (ptp90) REVERT: D 1118 ASP cc_start: 0.5950 (m-30) cc_final: 0.5431 (m-30) REVERT: D 1119 LYS cc_start: 0.6583 (tttm) cc_final: 0.5971 (ttpp) REVERT: D 1122 ARG cc_start: 0.5994 (mtm-85) cc_final: 0.5347 (mtm-85) REVERT: D 1124 TRP cc_start: 0.6231 (t60) cc_final: 0.5908 (t60) REVERT: D 1128 ARG cc_start: 0.5355 (ttp80) cc_final: 0.4612 (tpt-90) REVERT: D 1131 MET cc_start: 0.5616 (mmp) cc_final: 0.5322 (mtm) REVERT: D 1133 GLU cc_start: 0.6295 (mm-30) cc_final: 0.6024 (mp0) REVERT: D 1154 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6276 (mt) REVERT: D 1156 HIS cc_start: 0.4844 (m90) cc_final: 0.4568 (m-70) REVERT: D 1199 ARG cc_start: 0.6803 (tpp-160) cc_final: 0.6318 (tpt170) REVERT: D 1200 LEU cc_start: 0.6784 (tp) cc_final: 0.6549 (tp) REVERT: D 1222 GLU cc_start: 0.7028 (tt0) cc_final: 0.6424 (tp30) REVERT: D 1394 MET cc_start: 0.6918 (mmm) cc_final: 0.6665 (mtp) REVERT: D 1459 ASP cc_start: 0.6230 (t0) cc_final: 0.5875 (m-30) outliers start: 4 outliers final: 0 residues processed: 961 average time/residue: 0.8595 time to fit residues: 995.1008 Evaluate side-chains 730 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 726 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain D residue 1154 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.5980 chunk 223 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN A 253 ASN A 450 ASN A 702 ASN A1456 GLN B 132 GLN B 253 ASN B 450 ASN B 702 ASN B1129 GLN B1456 GLN C 132 GLN C 253 ASN C 450 ASN C 702 ASN C1129 GLN C1456 GLN D 132 GLN D 253 ASN D 450 ASN D 702 ASN D1129 GLN D1456 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.178943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144545 restraints weight = 42153.663| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.31 r_work: 0.3395 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43736 Z= 0.128 Angle : 0.523 6.376 59468 Z= 0.275 Chirality : 0.039 0.140 6728 Planarity : 0.004 0.035 7572 Dihedral : 7.272 128.271 6828 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.24 % Allowed : 7.65 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.11), residues: 5468 helix: 2.05 (0.09), residues: 3024 sheet: -0.66 (0.21), residues: 464 loop : -0.08 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 617 TYR 0.017 0.002 TYR B1232 PHE 0.013 0.002 PHE C 879 TRP 0.010 0.001 TRP D1124 HIS 0.007 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (43732) covalent geometry : angle 0.52311 / 0.27 (59460) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 0.34881 / 0.22 ( 8) hydrogen bonds : bond 0.04445 / 2.96 ( 2372) hydrogen bonds : angle 4.07770 / 2.96 ( 6984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 689 time to evaluate : 1.598 Fit side-chains REVERT: A 55 LYS cc_start: 0.7014 (mttt) cc_final: 0.6656 (mptt) REVERT: A 60 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6222 (mt-10) REVERT: A 129 MET cc_start: 0.8465 (mmp) cc_final: 0.8205 (mmp) REVERT: A 166 LYS cc_start: 0.7712 (tttm) cc_final: 0.7164 (mptt) REVERT: A 173 GLN cc_start: 0.7020 (pt0) cc_final: 0.6699 (tm-30) REVERT: A 174 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6859 (mtt180) REVERT: A 371 ASP cc_start: 0.7194 (t70) cc_final: 0.6937 (m-30) REVERT: A 381 ASN cc_start: 0.7869 (m-40) cc_final: 0.7639 (m110) REVERT: A 402 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7485 (tttp) REVERT: A 413 ASN cc_start: 0.7446 (m-40) cc_final: 0.7181 (m-40) REVERT: A 464 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6631 (mt-10) REVERT: A 498 LEU cc_start: 0.7688 (mt) cc_final: 0.7446 (mp) REVERT: A 506 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6560 (tmm160) REVERT: A 507 GLU cc_start: 0.7051 (tp30) cc_final: 0.6770 (tp30) REVERT: A 516 GLN cc_start: 0.6807 (tt0) cc_final: 0.6332 (pp30) REVERT: A 517 ARG cc_start: 0.6314 (mtp180) cc_final: 0.5914 (mtp85) REVERT: A 571 ASP cc_start: 0.5590 (p0) cc_final: 0.5207 (t70) REVERT: A 615 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7869 (tpp) REVERT: A 638 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6410 (mt-10) REVERT: A 657 LYS cc_start: 0.7279 (ttpp) cc_final: 0.6923 (ttpt) REVERT: A 659 GLN cc_start: 0.7290 (mt0) cc_final: 0.6750 (mt0) REVERT: A 663 LYS cc_start: 0.7934 (tptm) cc_final: 0.7710 (mtpt) REVERT: A 694 MET cc_start: 0.5269 (mtm) cc_final: 0.5021 (pmm) REVERT: A 729 HIS cc_start: 0.5999 (m90) cc_final: 0.5771 (m-70) REVERT: A 916 ARG cc_start: 0.8106 (tpm170) cc_final: 0.7887 (tmm-80) REVERT: A 920 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7527 (tp) REVERT: A 969 ARG cc_start: 0.8437 (mtm110) cc_final: 0.8039 (mtm-85) REVERT: A 989 ASP cc_start: 0.8417 (m-30) cc_final: 0.8095 (p0) REVERT: A 1042 MET cc_start: 0.8547 (mtm) cc_final: 0.8238 (mmm) REVERT: A 1046 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 1065 ASP cc_start: 0.6943 (m-30) cc_final: 0.6681 (m-30) REVERT: A 1079 VAL cc_start: 0.6656 (m) cc_final: 0.6345 (p) REVERT: A 1081 MET cc_start: 0.6382 (mtm) cc_final: 0.5966 (mtp) REVERT: A 1122 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6919 (mtm-85) REVERT: A 1123 ARG cc_start: 0.7359 (ttp80) cc_final: 0.7135 (ttp80) REVERT: A 1124 TRP cc_start: 0.7468 (t60) cc_final: 0.7133 (t60) REVERT: A 1128 ARG cc_start: 0.6407 (ttp80) cc_final: 0.5761 (tpt-90) REVERT: A 1151 ASP cc_start: 0.7278 (m-30) cc_final: 0.7074 (m-30) REVERT: A 1199 ARG cc_start: 0.6789 (tpp-160) cc_final: 0.6563 (tpt170) REVERT: A 1389 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 1407 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: B 55 LYS cc_start: 0.7022 (mttt) cc_final: 0.6662 (mptt) REVERT: B 60 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6214 (mt-10) REVERT: B 129 MET cc_start: 0.8457 (mmp) cc_final: 0.8204 (mmp) REVERT: B 166 LYS cc_start: 0.7692 (tttm) cc_final: 0.7152 (mptt) REVERT: B 173 GLN cc_start: 0.7017 (pt0) cc_final: 0.6695 (tm-30) REVERT: B 371 ASP cc_start: 0.7190 (t70) cc_final: 0.6933 (m-30) REVERT: B 381 ASN cc_start: 0.7873 (m-40) cc_final: 0.7637 (m110) REVERT: B 413 ASN cc_start: 0.7466 (m-40) cc_final: 0.7181 (m-40) REVERT: B 464 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6686 (mt-10) REVERT: B 498 LEU cc_start: 0.7689 (mt) cc_final: 0.7445 (mp) REVERT: B 506 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.6580 (tmm160) REVERT: B 516 GLN cc_start: 0.6801 (tt0) cc_final: 0.6329 (pp30) REVERT: B 517 ARG cc_start: 0.6330 (mtp180) cc_final: 0.5925 (mtp85) REVERT: B 615 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7876 (tpp) REVERT: B 638 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6432 (mt-10) REVERT: B 657 LYS cc_start: 0.7320 (ttpp) cc_final: 0.6963 (ttpt) REVERT: B 659 GLN cc_start: 0.7267 (mt0) cc_final: 0.6738 (mt0) REVERT: B 663 LYS cc_start: 0.7933 (tptm) cc_final: 0.7702 (mtpt) REVERT: B 694 MET cc_start: 0.5296 (mtm) cc_final: 0.5038 (pmm) REVERT: B 729 HIS cc_start: 0.6017 (m90) cc_final: 0.5791 (m-70) REVERT: B 916 ARG cc_start: 0.8117 (tpm170) cc_final: 0.7894 (tmm-80) REVERT: B 920 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7519 (tp) REVERT: B 969 ARG cc_start: 0.8441 (mtm110) cc_final: 0.8042 (mtm-85) REVERT: B 989 ASP cc_start: 0.8423 (m-30) cc_final: 0.8100 (p0) REVERT: B 1042 MET cc_start: 0.8540 (mtm) cc_final: 0.8236 (mmm) REVERT: B 1046 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: B 1065 ASP cc_start: 0.6941 (m-30) cc_final: 0.6676 (m-30) REVERT: B 1079 VAL cc_start: 0.6652 (m) cc_final: 0.6336 (p) REVERT: B 1081 MET cc_start: 0.6379 (mtm) cc_final: 0.5959 (mtp) REVERT: B 1122 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: B 1123 ARG cc_start: 0.7370 (ttp80) cc_final: 0.7141 (ttp80) REVERT: B 1124 TRP cc_start: 0.7485 (t60) cc_final: 0.7139 (t60) REVERT: B 1128 ARG cc_start: 0.6397 (ttp80) cc_final: 0.5760 (tpt-90) REVERT: B 1150 MET cc_start: 0.7523 (mtm) cc_final: 0.7271 (mtt) REVERT: B 1151 ASP cc_start: 0.7274 (m-30) cc_final: 0.7069 (m-30) REVERT: B 1199 ARG cc_start: 0.6803 (tpp-160) cc_final: 0.6468 (tpt170) REVERT: B 1389 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 1407 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: C 55 LYS cc_start: 0.7005 (mttt) cc_final: 0.6650 (mptt) REVERT: C 60 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6203 (mt-10) REVERT: C 129 MET cc_start: 0.8454 (mmp) cc_final: 0.8201 (mmp) REVERT: C 166 LYS cc_start: 0.7700 (tttm) cc_final: 0.7160 (mptt) REVERT: C 173 GLN cc_start: 0.7024 (pt0) cc_final: 0.6702 (tm-30) REVERT: C 371 ASP cc_start: 0.7186 (t70) cc_final: 0.6925 (m-30) REVERT: C 381 ASN cc_start: 0.7873 (m-40) cc_final: 0.7641 (m110) REVERT: C 413 ASN cc_start: 0.7470 (m-40) cc_final: 0.7207 (m-40) REVERT: C 464 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6643 (mt-10) REVERT: C 498 LEU cc_start: 0.7683 (mt) cc_final: 0.7439 (mp) REVERT: C 506 ARG cc_start: 0.7128 (ttt-90) cc_final: 0.6571 (tmm160) REVERT: C 516 GLN cc_start: 0.6794 (tt0) cc_final: 0.6319 (pp30) REVERT: C 517 ARG cc_start: 0.6322 (mtp180) cc_final: 0.5919 (mtp85) REVERT: C 615 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7874 (tpp) REVERT: C 638 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6429 (mt-10) REVERT: C 657 LYS cc_start: 0.7321 (ttpp) cc_final: 0.6966 (ttpt) REVERT: C 659 GLN cc_start: 0.7277 (mt0) cc_final: 0.6746 (mt0) REVERT: C 663 LYS cc_start: 0.7934 (tptm) cc_final: 0.7701 (mtpt) REVERT: C 694 MET cc_start: 0.5274 (mtm) cc_final: 0.5031 (pmm) REVERT: C 729 HIS cc_start: 0.6011 (m90) cc_final: 0.5785 (m-70) REVERT: C 916 ARG cc_start: 0.8110 (tpm170) cc_final: 0.7887 (tmm-80) REVERT: C 920 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7518 (tp) REVERT: C 969 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8037 (mtm-85) REVERT: C 989 ASP cc_start: 0.8420 (m-30) cc_final: 0.8085 (p0) REVERT: C 1042 MET cc_start: 0.8542 (mtm) cc_final: 0.8236 (mmm) REVERT: C 1046 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 1065 ASP cc_start: 0.6938 (m-30) cc_final: 0.6670 (m-30) REVERT: C 1079 VAL cc_start: 0.6657 (m) cc_final: 0.6342 (p) REVERT: C 1081 MET cc_start: 0.6390 (mtm) cc_final: 0.5971 (mtp) REVERT: C 1122 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6932 (mtm-85) REVERT: C 1123 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7152 (ttp80) REVERT: C 1124 TRP cc_start: 0.7490 (t60) cc_final: 0.7145 (t60) REVERT: C 1128 ARG cc_start: 0.6396 (ttp80) cc_final: 0.5760 (tpt-90) REVERT: C 1150 MET cc_start: 0.7517 (mtm) cc_final: 0.7259 (mtt) REVERT: C 1151 ASP cc_start: 0.7277 (m-30) cc_final: 0.7072 (m-30) REVERT: C 1157 MET cc_start: 0.7188 (mtp) cc_final: 0.6580 (mtt) REVERT: C 1199 ARG cc_start: 0.6838 (tpp-160) cc_final: 0.6610 (tpt170) REVERT: C 1389 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 1407 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6610 (m-30) REVERT: D 55 LYS cc_start: 0.7013 (mttt) cc_final: 0.6655 (mptt) REVERT: D 60 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6187 (mt-10) REVERT: D 129 MET cc_start: 0.8454 (mmp) cc_final: 0.8199 (mmp) REVERT: D 166 LYS cc_start: 0.7713 (tttm) cc_final: 0.7166 (mptt) REVERT: D 173 GLN cc_start: 0.7019 (pt0) cc_final: 0.6696 (tm-30) REVERT: D 371 ASP cc_start: 0.7191 (t70) cc_final: 0.6936 (m-30) REVERT: D 381 ASN cc_start: 0.7856 (m-40) cc_final: 0.7623 (m110) REVERT: D 413 ASN cc_start: 0.7461 (m-40) cc_final: 0.7200 (m-40) REVERT: D 464 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6635 (mt-10) REVERT: D 498 LEU cc_start: 0.7682 (mt) cc_final: 0.7440 (mp) REVERT: D 506 ARG cc_start: 0.7130 (ttt-90) cc_final: 0.6566 (tmm160) REVERT: D 516 GLN cc_start: 0.6798 (tt0) cc_final: 0.6319 (pp30) REVERT: D 517 ARG cc_start: 0.6322 (mtp180) cc_final: 0.5919 (mtp85) REVERT: D 615 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7869 (tpp) REVERT: D 638 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6420 (mt-10) REVERT: D 657 LYS cc_start: 0.7311 (ttpp) cc_final: 0.6955 (ttpt) REVERT: D 659 GLN cc_start: 0.7284 (mt0) cc_final: 0.6750 (mt0) REVERT: D 663 LYS cc_start: 0.7937 (tptm) cc_final: 0.7700 (mtpt) REVERT: D 694 MET cc_start: 0.5292 (mtm) cc_final: 0.5033 (pmm) REVERT: D 729 HIS cc_start: 0.6013 (m90) cc_final: 0.5788 (m-70) REVERT: D 916 ARG cc_start: 0.8111 (tpm170) cc_final: 0.7887 (tmm-80) REVERT: D 920 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7522 (tp) REVERT: D 969 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8039 (mtm-85) REVERT: D 989 ASP cc_start: 0.8421 (m-30) cc_final: 0.8077 (p0) REVERT: D 1042 MET cc_start: 0.8553 (mtm) cc_final: 0.8239 (mmm) REVERT: D 1046 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: D 1065 ASP cc_start: 0.6949 (m-30) cc_final: 0.6683 (m-30) REVERT: D 1079 VAL cc_start: 0.6652 (m) cc_final: 0.6336 (p) REVERT: D 1081 MET cc_start: 0.6392 (mtm) cc_final: 0.5973 (mtp) REVERT: D 1122 ARG cc_start: 0.7275 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: D 1123 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7137 (ttp80) REVERT: D 1124 TRP cc_start: 0.7478 (t60) cc_final: 0.7134 (t60) REVERT: D 1128 ARG cc_start: 0.6387 (ttp80) cc_final: 0.5757 (tpt-90) REVERT: D 1150 MET cc_start: 0.7518 (mtm) cc_final: 0.7274 (mtt) REVERT: D 1151 ASP cc_start: 0.7279 (m-30) cc_final: 0.7059 (m-30) REVERT: D 1199 ARG cc_start: 0.6832 (tpp-160) cc_final: 0.6606 (tpt170) REVERT: D 1389 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7535 (mt-10) REVERT: D 1407 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6578 (m-30) outliers start: 53 outliers final: 8 residues processed: 706 average time/residue: 0.8865 time to fit residues: 749.4341 Evaluate side-chains 597 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 573 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain B residue 1407 ASP Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1405 SER Chi-restraints excluded: chain D residue 1407 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 297 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 454 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 332 optimal weight: 0.0370 chunk 407 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 383 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 689 HIS C1152 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141484 restraints weight = 41861.502| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.34 r_work: 0.3356 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 43736 Z= 0.123 Angle : 0.502 6.238 59468 Z= 0.264 Chirality : 0.038 0.146 6728 Planarity : 0.004 0.043 7572 Dihedral : 6.699 124.257 6820 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.42 % Allowed : 8.84 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.11), residues: 5468 helix: 2.26 (0.09), residues: 3052 sheet: -0.68 (0.21), residues: 472 loop : 0.03 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1347 TYR 0.016 0.002 TYR B1063 PHE 0.019 0.002 PHE B 879 TRP 0.011 0.001 TRP A1366 HIS 0.006 0.001 HIS B 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (43732) covalent geometry : angle 0.50166 / 0.26 (59460) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.29050 / 0.18 ( 8) hydrogen bonds : bond 0.04265 / 2.85 ( 2372) hydrogen bonds : angle 3.93020 / 2.85 ( 6984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 632 time to evaluate : 1.785 Fit side-chains REVERT: A 55 LYS cc_start: 0.7135 (mttt) cc_final: 0.6855 (mppt) REVERT: A 60 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6191 (mt-10) REVERT: A 129 MET cc_start: 0.8516 (mmp) cc_final: 0.8218 (mmp) REVERT: A 132 GLN cc_start: 0.7366 (tt0) cc_final: 0.7046 (tp-100) REVERT: A 166 LYS cc_start: 0.7787 (tttm) cc_final: 0.7250 (mptt) REVERT: A 371 ASP cc_start: 0.7271 (t70) cc_final: 0.6963 (m-30) REVERT: A 381 ASN cc_start: 0.7801 (m-40) cc_final: 0.7557 (m110) REVERT: A 413 ASN cc_start: 0.7427 (m-40) cc_final: 0.7108 (m-40) REVERT: A 464 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6624 (mt-10) REVERT: A 502 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7346 (tt0) REVERT: A 506 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6468 (tmm160) REVERT: A 516 GLN cc_start: 0.6978 (tt0) cc_final: 0.6623 (tm130) REVERT: A 517 ARG cc_start: 0.6423 (mtp180) cc_final: 0.6068 (mtp85) REVERT: A 571 ASP cc_start: 0.5471 (p0) cc_final: 0.5241 (t70) REVERT: A 638 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6497 (mt-10) REVERT: A 657 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6932 (ttpt) REVERT: A 659 GLN cc_start: 0.7336 (mt0) cc_final: 0.6813 (mt0) REVERT: A 663 LYS cc_start: 0.8086 (tptm) cc_final: 0.7853 (ttmt) REVERT: A 969 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8138 (mtm-85) REVERT: A 1042 MET cc_start: 0.8587 (mtm) cc_final: 0.8285 (mmm) REVERT: A 1046 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: A 1065 ASP cc_start: 0.7184 (m-30) cc_final: 0.6939 (m-30) REVERT: A 1079 VAL cc_start: 0.6696 (m) cc_final: 0.6466 (p) REVERT: A 1081 MET cc_start: 0.6466 (mtm) cc_final: 0.6025 (mtt) REVERT: A 1122 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6866 (mtm-85) REVERT: A 1123 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6865 (ttt90) REVERT: A 1124 TRP cc_start: 0.7435 (t60) cc_final: 0.7027 (t60) REVERT: A 1128 ARG cc_start: 0.6419 (ttp80) cc_final: 0.5761 (tpt-90) REVERT: A 1151 ASP cc_start: 0.7481 (m-30) cc_final: 0.7254 (m-30) REVERT: A 1389 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7866 (mt-10) REVERT: B 55 LYS cc_start: 0.7155 (mttt) cc_final: 0.6871 (mppt) REVERT: B 60 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6160 (mt-10) REVERT: B 116 ASN cc_start: 0.6976 (m-40) cc_final: 0.6599 (m110) REVERT: B 129 MET cc_start: 0.8511 (mmp) cc_final: 0.8213 (mmp) REVERT: B 132 GLN cc_start: 0.7372 (tt0) cc_final: 0.7043 (tp-100) REVERT: B 166 LYS cc_start: 0.7785 (tttm) cc_final: 0.7246 (mptt) REVERT: B 371 ASP cc_start: 0.7268 (t70) cc_final: 0.6961 (m-30) REVERT: B 381 ASN cc_start: 0.7807 (m-40) cc_final: 0.7561 (m110) REVERT: B 413 ASN cc_start: 0.7434 (m-40) cc_final: 0.7076 (m-40) REVERT: B 464 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6590 (mt-10) REVERT: B 502 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7349 (tt0) REVERT: B 506 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6469 (tmm160) REVERT: B 516 GLN cc_start: 0.6979 (tt0) cc_final: 0.6624 (tm130) REVERT: B 517 ARG cc_start: 0.6429 (mtp180) cc_final: 0.6072 (mtp85) REVERT: B 638 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6488 (mt-10) REVERT: B 657 LYS cc_start: 0.7247 (ttpp) cc_final: 0.6955 (ttpt) REVERT: B 659 GLN cc_start: 0.7305 (mt0) cc_final: 0.6785 (mt0) REVERT: B 663 LYS cc_start: 0.8082 (tptm) cc_final: 0.7858 (ttmt) REVERT: B 969 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8134 (mtm-85) REVERT: B 1042 MET cc_start: 0.8577 (mtm) cc_final: 0.8280 (mmm) REVERT: B 1046 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: B 1065 ASP cc_start: 0.7183 (m-30) cc_final: 0.6921 (m-30) REVERT: B 1079 VAL cc_start: 0.6696 (m) cc_final: 0.6462 (p) REVERT: B 1081 MET cc_start: 0.6483 (mtm) cc_final: 0.6040 (mtt) REVERT: B 1122 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.6873 (mtm-85) REVERT: B 1123 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6858 (ttt90) REVERT: B 1124 TRP cc_start: 0.7438 (t60) cc_final: 0.7027 (t60) REVERT: B 1128 ARG cc_start: 0.6442 (ttp80) cc_final: 0.5791 (tpt-90) REVERT: B 1151 ASP cc_start: 0.7444 (m-30) cc_final: 0.7228 (m-30) REVERT: B 1389 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7863 (mt-10) REVERT: C 55 LYS cc_start: 0.7145 (mttt) cc_final: 0.6868 (mppt) REVERT: C 60 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6157 (mt-10) REVERT: C 116 ASN cc_start: 0.6991 (m-40) cc_final: 0.6617 (m110) REVERT: C 129 MET cc_start: 0.8512 (mmp) cc_final: 0.8214 (mmp) REVERT: C 132 GLN cc_start: 0.7369 (tt0) cc_final: 0.7043 (tp-100) REVERT: C 166 LYS cc_start: 0.7787 (tttm) cc_final: 0.7249 (mptt) REVERT: C 371 ASP cc_start: 0.7253 (t70) cc_final: 0.6953 (m-30) REVERT: C 381 ASN cc_start: 0.7820 (m-40) cc_final: 0.7574 (m110) REVERT: C 413 ASN cc_start: 0.7426 (m-40) cc_final: 0.7069 (m-40) REVERT: C 464 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6584 (mt-10) REVERT: C 502 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7354 (tt0) REVERT: C 506 ARG cc_start: 0.7078 (ttt-90) cc_final: 0.6468 (tmm160) REVERT: C 516 GLN cc_start: 0.6968 (tt0) cc_final: 0.6615 (tm130) REVERT: C 517 ARG cc_start: 0.6420 (mtp180) cc_final: 0.6063 (mtp85) REVERT: C 571 ASP cc_start: 0.5466 (p0) cc_final: 0.5231 (t70) REVERT: C 638 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6493 (mt-10) REVERT: C 657 LYS cc_start: 0.7246 (ttpp) cc_final: 0.6953 (ttpt) REVERT: C 659 GLN cc_start: 0.7291 (mt0) cc_final: 0.6767 (mt0) REVERT: C 663 LYS cc_start: 0.8090 (tptm) cc_final: 0.7857 (ttmt) REVERT: C 969 ARG cc_start: 0.8430 (mtm110) cc_final: 0.8138 (mtm-85) REVERT: C 1042 MET cc_start: 0.8585 (mtm) cc_final: 0.8282 (mmm) REVERT: C 1046 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: C 1065 ASP cc_start: 0.7183 (m-30) cc_final: 0.6922 (m-30) REVERT: C 1079 VAL cc_start: 0.6700 (m) cc_final: 0.6467 (p) REVERT: C 1081 MET cc_start: 0.6493 (mtm) cc_final: 0.6051 (mtt) REVERT: C 1122 ARG cc_start: 0.7275 (mtm-85) cc_final: 0.6870 (mtm-85) REVERT: C 1123 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6857 (ttt90) REVERT: C 1124 TRP cc_start: 0.7438 (t60) cc_final: 0.7022 (t60) REVERT: C 1128 ARG cc_start: 0.6430 (ttp80) cc_final: 0.5786 (tpt-90) REVERT: C 1150 MET cc_start: 0.7743 (mtm) cc_final: 0.7414 (mtm) REVERT: C 1151 ASP cc_start: 0.7432 (m-30) cc_final: 0.7230 (m-30) REVERT: C 1157 MET cc_start: 0.7244 (mtp) cc_final: 0.6901 (mtt) REVERT: C 1389 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7878 (mt-10) REVERT: D 55 LYS cc_start: 0.7125 (mttt) cc_final: 0.6843 (mppt) REVERT: D 60 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6155 (mt-10) REVERT: D 129 MET cc_start: 0.8509 (mmp) cc_final: 0.8210 (mmp) REVERT: D 132 GLN cc_start: 0.7361 (tt0) cc_final: 0.7037 (tp-100) REVERT: D 166 LYS cc_start: 0.7784 (tttm) cc_final: 0.7239 (mptt) REVERT: D 371 ASP cc_start: 0.7291 (t70) cc_final: 0.6991 (m-30) REVERT: D 381 ASN cc_start: 0.7804 (m-40) cc_final: 0.7558 (m110) REVERT: D 413 ASN cc_start: 0.7420 (m-40) cc_final: 0.7064 (m-40) REVERT: D 464 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6585 (mt-10) REVERT: D 502 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7356 (tt0) REVERT: D 506 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6465 (tmm160) REVERT: D 516 GLN cc_start: 0.6969 (tt0) cc_final: 0.6612 (tm130) REVERT: D 517 ARG cc_start: 0.6417 (mtp180) cc_final: 0.6060 (mtp85) REVERT: D 571 ASP cc_start: 0.5467 (p0) cc_final: 0.5229 (t70) REVERT: D 638 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6495 (mt-10) REVERT: D 657 LYS cc_start: 0.7243 (ttpp) cc_final: 0.6949 (ttpt) REVERT: D 659 GLN cc_start: 0.7299 (mt0) cc_final: 0.6776 (mt0) REVERT: D 663 LYS cc_start: 0.8086 (tptm) cc_final: 0.7854 (ttmt) REVERT: D 969 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8132 (mtm-85) REVERT: D 1042 MET cc_start: 0.8588 (mtm) cc_final: 0.8284 (mmm) REVERT: D 1046 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: D 1065 ASP cc_start: 0.7181 (m-30) cc_final: 0.6920 (m-30) REVERT: D 1079 VAL cc_start: 0.6696 (m) cc_final: 0.6464 (p) REVERT: D 1081 MET cc_start: 0.6489 (mtm) cc_final: 0.6049 (mtt) REVERT: D 1122 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: D 1123 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6859 (ttt90) REVERT: D 1124 TRP cc_start: 0.7439 (t60) cc_final: 0.7027 (t60) REVERT: D 1128 ARG cc_start: 0.6431 (ttp80) cc_final: 0.5785 (tpt-90) REVERT: D 1150 MET cc_start: 0.7747 (mtm) cc_final: 0.7523 (mtt) REVERT: D 1151 ASP cc_start: 0.7446 (m-30) cc_final: 0.7228 (m-30) REVERT: D 1389 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7870 (mt-10) outliers start: 103 outliers final: 44 residues processed: 683 average time/residue: 0.8679 time to fit residues: 713.1289 Evaluate side-chains 619 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 571 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1263 VAL Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1263 VAL Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1200 LEU Chi-restraints excluded: chain D residue 1263 VAL Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 482 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 308 optimal weight: 0.4980 chunk 197 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 406 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 332 optimal weight: 9.9990 chunk 353 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.175484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141881 restraints weight = 41803.303| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.46 r_work: 0.3334 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43736 Z= 0.112 Angle : 0.480 6.769 59468 Z= 0.250 Chirality : 0.038 0.141 6728 Planarity : 0.004 0.039 7572 Dihedral : 6.537 123.467 6820 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.06 % Allowed : 10.34 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.11), residues: 5468 helix: 2.38 (0.09), residues: 3040 sheet: -0.65 (0.21), residues: 468 loop : 0.02 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 152 TYR 0.016 0.002 TYR A1232 PHE 0.018 0.002 PHE B 879 TRP 0.011 0.001 TRP B1366 HIS 0.006 0.001 HIS B 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (43732) covalent geometry : angle 0.48039 / 0.25 (59460) SS BOND : bond 0.00008 / 0.00 ( 4) SS BOND : angle 0.18122 / 0.11 ( 8) hydrogen bonds : bond 0.04006 / 2.67 ( 2372) hydrogen bonds : angle 3.82678 / 2.78 ( 6984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 612 time to evaluate : 1.469 Fit side-chains REVERT: A 55 LYS cc_start: 0.7107 (mttt) cc_final: 0.6757 (mptt) REVERT: A 60 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6213 (mt-10) REVERT: A 129 MET cc_start: 0.8518 (mmp) cc_final: 0.8220 (mmp) REVERT: A 132 GLN cc_start: 0.7456 (tt0) cc_final: 0.7176 (tp40) REVERT: A 166 LYS cc_start: 0.7746 (tttm) cc_final: 0.7220 (mptp) REVERT: A 371 ASP cc_start: 0.7317 (t70) cc_final: 0.6980 (m-30) REVERT: A 381 ASN cc_start: 0.7798 (m-40) cc_final: 0.7547 (m110) REVERT: A 413 ASN cc_start: 0.7500 (m-40) cc_final: 0.7170 (m-40) REVERT: A 464 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6461 (mt-10) REVERT: A 502 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7325 (tt0) REVERT: A 506 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6431 (tmm160) REVERT: A 516 GLN cc_start: 0.7003 (tt0) cc_final: 0.6738 (tm130) REVERT: A 517 ARG cc_start: 0.6414 (mtp180) cc_final: 0.6003 (mtp85) REVERT: A 638 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6522 (mt-10) REVERT: A 657 LYS cc_start: 0.7253 (ttpp) cc_final: 0.6970 (ttpt) REVERT: A 659 GLN cc_start: 0.7292 (mt0) cc_final: 0.6780 (mt0) REVERT: A 663 LYS cc_start: 0.8099 (tptm) cc_final: 0.7766 (mtpt) REVERT: A 667 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: A 916 ARG cc_start: 0.8176 (tpm170) cc_final: 0.7885 (tmm-80) REVERT: A 969 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8102 (mtm-85) REVERT: A 1042 MET cc_start: 0.8545 (mtm) cc_final: 0.8202 (mmm) REVERT: A 1046 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: A 1065 ASP cc_start: 0.7270 (m-30) cc_final: 0.7007 (m-30) REVERT: A 1081 MET cc_start: 0.6440 (mtm) cc_final: 0.6045 (mtt) REVERT: A 1122 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6884 (mtm-85) REVERT: A 1124 TRP cc_start: 0.7412 (t60) cc_final: 0.6964 (t60) REVERT: A 1128 ARG cc_start: 0.6366 (ttp80) cc_final: 0.5711 (tpt-90) REVERT: A 1151 ASP cc_start: 0.7580 (m-30) cc_final: 0.7322 (m-30) REVERT: A 1389 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 55 LYS cc_start: 0.7111 (mttt) cc_final: 0.6764 (mptt) REVERT: B 60 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6207 (mt-10) REVERT: B 129 MET cc_start: 0.8506 (mmp) cc_final: 0.8207 (mmp) REVERT: B 132 GLN cc_start: 0.7445 (tt0) cc_final: 0.7172 (tp40) REVERT: B 166 LYS cc_start: 0.7745 (tttm) cc_final: 0.7218 (mptp) REVERT: B 371 ASP cc_start: 0.7324 (t70) cc_final: 0.6986 (m-30) REVERT: B 381 ASN cc_start: 0.7813 (m-40) cc_final: 0.7561 (m110) REVERT: B 413 ASN cc_start: 0.7507 (m-40) cc_final: 0.7152 (m-40) REVERT: B 464 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6481 (mt-10) REVERT: B 502 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7344 (tt0) REVERT: B 506 ARG cc_start: 0.7107 (ttt-90) cc_final: 0.6437 (tmm160) REVERT: B 516 GLN cc_start: 0.6988 (tt0) cc_final: 0.6731 (tm130) REVERT: B 517 ARG cc_start: 0.6422 (mtp180) cc_final: 0.6006 (mtp85) REVERT: B 523 ASN cc_start: 0.5967 (m-40) cc_final: 0.5284 (p0) REVERT: B 638 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6486 (mt-10) REVERT: B 657 LYS cc_start: 0.7254 (ttpp) cc_final: 0.6971 (ttpt) REVERT: B 659 GLN cc_start: 0.7283 (mt0) cc_final: 0.6772 (mt0) REVERT: B 663 LYS cc_start: 0.8071 (tptm) cc_final: 0.7739 (mtpt) REVERT: B 667 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: B 916 ARG cc_start: 0.8175 (tpm170) cc_final: 0.7888 (tmm-80) REVERT: B 969 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8100 (mtm-85) REVERT: B 1042 MET cc_start: 0.8597 (mtm) cc_final: 0.8268 (mmm) REVERT: B 1046 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: B 1065 ASP cc_start: 0.7260 (m-30) cc_final: 0.6998 (m-30) REVERT: B 1081 MET cc_start: 0.6431 (mtm) cc_final: 0.6033 (mtt) REVERT: B 1122 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6871 (mtm-85) REVERT: B 1124 TRP cc_start: 0.7414 (t60) cc_final: 0.6966 (t60) REVERT: B 1128 ARG cc_start: 0.6393 (ttp80) cc_final: 0.5749 (tpt-90) REVERT: B 1151 ASP cc_start: 0.7467 (m-30) cc_final: 0.7226 (m-30) REVERT: B 1389 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7944 (mt-10) REVERT: C 55 LYS cc_start: 0.7102 (mttt) cc_final: 0.6751 (mptt) REVERT: C 60 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6187 (mt-10) REVERT: C 129 MET cc_start: 0.8512 (mmp) cc_final: 0.8214 (mmp) REVERT: C 132 GLN cc_start: 0.7428 (tt0) cc_final: 0.7168 (tp40) REVERT: C 166 LYS cc_start: 0.7740 (tttm) cc_final: 0.7212 (mptp) REVERT: C 371 ASP cc_start: 0.7329 (t70) cc_final: 0.6987 (m-30) REVERT: C 381 ASN cc_start: 0.7819 (m-40) cc_final: 0.7567 (m110) REVERT: C 413 ASN cc_start: 0.7503 (m-40) cc_final: 0.7147 (m-40) REVERT: C 464 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6459 (mt-10) REVERT: C 502 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7342 (tt0) REVERT: C 506 ARG cc_start: 0.7097 (ttt-90) cc_final: 0.6436 (tmm160) REVERT: C 516 GLN cc_start: 0.6984 (tt0) cc_final: 0.6724 (tm130) REVERT: C 517 ARG cc_start: 0.6414 (mtp180) cc_final: 0.5997 (mtp85) REVERT: C 638 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6510 (mt-10) REVERT: C 657 LYS cc_start: 0.7256 (ttpp) cc_final: 0.6971 (ttpt) REVERT: C 659 GLN cc_start: 0.7286 (mt0) cc_final: 0.6772 (mt0) REVERT: C 663 LYS cc_start: 0.8086 (tptm) cc_final: 0.7749 (mtpt) REVERT: C 667 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: C 916 ARG cc_start: 0.8177 (tpm170) cc_final: 0.7888 (tmm-80) REVERT: C 969 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8108 (mtm-85) REVERT: C 1042 MET cc_start: 0.8596 (mtm) cc_final: 0.8265 (mmm) REVERT: C 1046 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: C 1065 ASP cc_start: 0.7258 (m-30) cc_final: 0.6995 (m-30) REVERT: C 1081 MET cc_start: 0.6447 (mtm) cc_final: 0.6048 (mtt) REVERT: C 1122 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6877 (mtm-85) REVERT: C 1124 TRP cc_start: 0.7429 (t60) cc_final: 0.6983 (t60) REVERT: C 1128 ARG cc_start: 0.6393 (ttp80) cc_final: 0.5748 (tpt-90) REVERT: C 1389 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7947 (mt-10) REVERT: D 55 LYS cc_start: 0.7136 (mttt) cc_final: 0.6766 (mptt) REVERT: D 60 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6188 (mt-10) REVERT: D 129 MET cc_start: 0.8507 (mmp) cc_final: 0.8208 (mmp) REVERT: D 132 GLN cc_start: 0.7427 (tt0) cc_final: 0.7163 (tp40) REVERT: D 166 LYS cc_start: 0.7744 (tttm) cc_final: 0.7216 (mptp) REVERT: D 371 ASP cc_start: 0.7309 (t70) cc_final: 0.6977 (m-30) REVERT: D 381 ASN cc_start: 0.7811 (m-40) cc_final: 0.7558 (m110) REVERT: D 413 ASN cc_start: 0.7498 (m-40) cc_final: 0.7144 (m-40) REVERT: D 464 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6453 (mt-10) REVERT: D 502 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7345 (tt0) REVERT: D 506 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6436 (tmm160) REVERT: D 516 GLN cc_start: 0.6979 (tt0) cc_final: 0.6719 (tm130) REVERT: D 517 ARG cc_start: 0.6406 (mtp180) cc_final: 0.5989 (mtp85) REVERT: D 638 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6515 (mt-10) REVERT: D 657 LYS cc_start: 0.7256 (ttpp) cc_final: 0.6970 (ttpt) REVERT: D 659 GLN cc_start: 0.7289 (mt0) cc_final: 0.6776 (mt0) REVERT: D 663 LYS cc_start: 0.8081 (tptm) cc_final: 0.7746 (mtpt) REVERT: D 667 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: D 916 ARG cc_start: 0.8176 (tpm170) cc_final: 0.7886 (tmm-80) REVERT: D 969 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8099 (mtm-85) REVERT: D 1042 MET cc_start: 0.8605 (mtm) cc_final: 0.8271 (mmm) REVERT: D 1046 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: D 1065 ASP cc_start: 0.7255 (m-30) cc_final: 0.6993 (m-30) REVERT: D 1081 MET cc_start: 0.6443 (mtm) cc_final: 0.6047 (mtt) REVERT: D 1122 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6871 (mtm-85) REVERT: D 1124 TRP cc_start: 0.7418 (t60) cc_final: 0.6973 (t60) REVERT: D 1128 ARG cc_start: 0.6393 (ttp80) cc_final: 0.5739 (tpt-90) REVERT: D 1151 ASP cc_start: 0.7543 (m-30) cc_final: 0.7325 (m-30) REVERT: D 1154 LEU cc_start: 0.7936 (mt) cc_final: 0.7703 (mt) REVERT: D 1389 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7948 (mt-10) outliers start: 88 outliers final: 44 residues processed: 654 average time/residue: 0.8316 time to fit residues: 654.9185 Evaluate side-chains 627 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 575 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1401 MET Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1401 MET Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1401 MET Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 5 optimal weight: 0.2980 chunk 489 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 512 optimal weight: 4.9990 chunk 528 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN A 364 GLN A 689 HIS A1129 GLN B 132 GLN B 185 ASN B 364 GLN B 689 HIS C 132 GLN C 185 ASN C 364 GLN C 689 HIS D 132 GLN D 185 ASN D 364 GLN D 689 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.173501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139138 restraints weight = 41807.896| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.41 r_work: 0.3301 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43736 Z= 0.164 Angle : 0.547 6.392 59468 Z= 0.288 Chirality : 0.040 0.144 6728 Planarity : 0.004 0.041 7572 Dihedral : 6.865 125.187 6820 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.51 % Allowed : 10.23 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.11), residues: 5468 helix: 2.15 (0.09), residues: 3080 sheet: -0.65 (0.21), residues: 468 loop : -0.16 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1385 TYR 0.022 0.002 TYR D 917 PHE 0.025 0.002 PHE B 879 TRP 0.013 0.002 TRP C1366 HIS 0.009 0.001 HIS D 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (43732) covalent geometry : angle 0.54710 / 0.29 (59460) SS BOND : bond 0.00028 / 0.01 ( 4) SS BOND : angle 0.19801 / 0.12 ( 8) hydrogen bonds : bond 0.04761 / 3.17 ( 2372) hydrogen bonds : angle 4.07043 / 2.96 ( 6984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 601 time to evaluate : 1.703 Fit side-chains REVERT: A 55 LYS cc_start: 0.7201 (mttt) cc_final: 0.6927 (mppt) REVERT: A 60 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6316 (mt-10) REVERT: A 132 GLN cc_start: 0.7518 (tt0) cc_final: 0.7219 (tp40) REVERT: A 139 ASP cc_start: 0.7357 (m-30) cc_final: 0.7085 (m-30) REVERT: A 166 LYS cc_start: 0.7633 (tttm) cc_final: 0.7207 (mptt) REVERT: A 239 MET cc_start: 0.6122 (ttm) cc_final: 0.5394 (tmm) REVERT: A 371 ASP cc_start: 0.7392 (t70) cc_final: 0.7010 (m-30) REVERT: A 395 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6554 (mp0) REVERT: A 464 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6554 (mt-10) REVERT: A 502 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7257 (tt0) REVERT: A 506 ARG cc_start: 0.7143 (ttt-90) cc_final: 0.6430 (tmm160) REVERT: A 516 GLN cc_start: 0.7060 (tt0) cc_final: 0.6738 (tm130) REVERT: A 517 ARG cc_start: 0.6483 (mtp180) cc_final: 0.6132 (mtp85) REVERT: A 638 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6534 (mt-10) REVERT: A 663 LYS cc_start: 0.8031 (tptm) cc_final: 0.7761 (ttmt) REVERT: A 667 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: A 969 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8097 (mtm-85) REVERT: A 1042 MET cc_start: 0.8557 (mtm) cc_final: 0.8202 (mmm) REVERT: A 1046 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: A 1122 ARG cc_start: 0.7281 (mtm-85) cc_final: 0.6612 (mtm-85) REVERT: A 1128 ARG cc_start: 0.6398 (ttp80) cc_final: 0.5687 (tpt-90) REVERT: A 1151 ASP cc_start: 0.7551 (m-30) cc_final: 0.7299 (m-30) REVERT: A 1200 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 55 LYS cc_start: 0.7213 (mttt) cc_final: 0.6940 (mppt) REVERT: B 60 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6326 (mt-10) REVERT: B 132 GLN cc_start: 0.7512 (tt0) cc_final: 0.7194 (tp40) REVERT: B 139 ASP cc_start: 0.7362 (m-30) cc_final: 0.7092 (m-30) REVERT: B 166 LYS cc_start: 0.7669 (tttm) cc_final: 0.7245 (mptt) REVERT: B 239 MET cc_start: 0.6113 (ttm) cc_final: 0.5405 (tmm) REVERT: B 371 ASP cc_start: 0.7391 (t70) cc_final: 0.7009 (m-30) REVERT: B 381 ASN cc_start: 0.7835 (m-40) cc_final: 0.7588 (m110) REVERT: B 395 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6556 (mp0) REVERT: B 413 ASN cc_start: 0.7491 (m-40) cc_final: 0.7048 (m110) REVERT: B 464 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6551 (mt-10) REVERT: B 502 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7260 (tt0) REVERT: B 506 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6437 (tmm160) REVERT: B 516 GLN cc_start: 0.7072 (tt0) cc_final: 0.6757 (tm130) REVERT: B 517 ARG cc_start: 0.6474 (mtp180) cc_final: 0.6124 (mtp85) REVERT: B 638 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6511 (mt-10) REVERT: B 657 LYS cc_start: 0.7221 (ttpp) cc_final: 0.6929 (ttpt) REVERT: B 663 LYS cc_start: 0.8011 (tptm) cc_final: 0.7752 (ttmt) REVERT: B 667 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: B 969 ARG cc_start: 0.8450 (mtm110) cc_final: 0.8089 (mtm-85) REVERT: B 1042 MET cc_start: 0.8555 (mtm) cc_final: 0.8198 (mmm) REVERT: B 1046 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: B 1122 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6594 (mtm-85) REVERT: B 1128 ARG cc_start: 0.6440 (ttp80) cc_final: 0.5742 (tpt-90) REVERT: B 1151 ASP cc_start: 0.7541 (m-30) cc_final: 0.7300 (m-30) REVERT: B 1200 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7727 (mp) REVERT: C 55 LYS cc_start: 0.7203 (mttt) cc_final: 0.6928 (mppt) REVERT: C 60 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6300 (mt-10) REVERT: C 132 GLN cc_start: 0.7511 (tt0) cc_final: 0.7207 (tp40) REVERT: C 139 ASP cc_start: 0.7360 (m-30) cc_final: 0.7089 (m-30) REVERT: C 166 LYS cc_start: 0.7671 (tttm) cc_final: 0.7248 (mptt) REVERT: C 239 MET cc_start: 0.6121 (ttm) cc_final: 0.5410 (tmm) REVERT: C 371 ASP cc_start: 0.7376 (t70) cc_final: 0.7000 (m-30) REVERT: C 381 ASN cc_start: 0.7844 (m-40) cc_final: 0.7596 (m110) REVERT: C 395 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6556 (mp0) REVERT: C 464 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6554 (mt-10) REVERT: C 502 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7260 (tt0) REVERT: C 506 ARG cc_start: 0.7144 (ttt-90) cc_final: 0.6436 (tmm160) REVERT: C 516 GLN cc_start: 0.7068 (tt0) cc_final: 0.6747 (tm130) REVERT: C 517 ARG cc_start: 0.6465 (mtp180) cc_final: 0.6113 (mtp85) REVERT: C 638 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6508 (mt-10) REVERT: C 657 LYS cc_start: 0.7219 (ttpp) cc_final: 0.6927 (ttpt) REVERT: C 663 LYS cc_start: 0.8013 (tptm) cc_final: 0.7748 (ttmt) REVERT: C 667 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: C 969 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8102 (mtm-85) REVERT: C 1042 MET cc_start: 0.8551 (mtm) cc_final: 0.8199 (mmm) REVERT: C 1046 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: C 1122 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6600 (mtm-85) REVERT: C 1128 ARG cc_start: 0.6453 (ttp80) cc_final: 0.5757 (tpt-90) REVERT: C 1151 ASP cc_start: 0.7693 (m-30) cc_final: 0.7387 (m-30) REVERT: C 1200 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7718 (mp) REVERT: D 55 LYS cc_start: 0.7205 (mttt) cc_final: 0.6926 (mppt) REVERT: D 60 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6318 (mt-10) REVERT: D 132 GLN cc_start: 0.7507 (tt0) cc_final: 0.7200 (tp40) REVERT: D 139 ASP cc_start: 0.7354 (m-30) cc_final: 0.7083 (m-30) REVERT: D 166 LYS cc_start: 0.7627 (tttm) cc_final: 0.7201 (mptt) REVERT: D 239 MET cc_start: 0.6134 (ttm) cc_final: 0.5410 (tmm) REVERT: D 371 ASP cc_start: 0.7395 (t70) cc_final: 0.7010 (m-30) REVERT: D 381 ASN cc_start: 0.7837 (m-40) cc_final: 0.7590 (m110) REVERT: D 395 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6552 (mp0) REVERT: D 464 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6556 (mt-10) REVERT: D 502 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7249 (tt0) REVERT: D 506 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6427 (tmm160) REVERT: D 516 GLN cc_start: 0.7071 (tt0) cc_final: 0.6747 (tm130) REVERT: D 517 ARG cc_start: 0.6469 (mtp180) cc_final: 0.6115 (mtp85) REVERT: D 638 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6527 (mt-10) REVERT: D 657 LYS cc_start: 0.7221 (ttpp) cc_final: 0.6927 (ttpt) REVERT: D 663 LYS cc_start: 0.8023 (tptm) cc_final: 0.7754 (ttmt) REVERT: D 667 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: D 969 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8096 (mtm-85) REVERT: D 1042 MET cc_start: 0.8556 (mtm) cc_final: 0.8200 (mmm) REVERT: D 1046 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: D 1122 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.6599 (mtm-85) REVERT: D 1128 ARG cc_start: 0.6452 (ttp80) cc_final: 0.5749 (tpt-90) REVERT: D 1151 ASP cc_start: 0.7616 (m-30) cc_final: 0.7330 (m-30) REVERT: D 1200 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7722 (mp) outliers start: 107 outliers final: 56 residues processed: 653 average time/residue: 0.8634 time to fit residues: 679.4554 Evaluate side-chains 631 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 563 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1401 MET Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1401 MET Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1200 LEU Chi-restraints excluded: chain D residue 1401 MET Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 518 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 chunk 539 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 470 optimal weight: 1.9990 chunk 448 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 352 GLN A1045 GLN A1292 HIS B 352 GLN B1045 GLN B1080 HIS B1156 HIS B1292 HIS C 352 GLN C1045 GLN C1080 HIS C1156 HIS C1292 HIS D 352 GLN D1045 GLN D1080 HIS D1292 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.172718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138227 restraints weight = 41506.921| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.33 r_work: 0.3305 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 43736 Z= 0.223 Angle : 0.636 6.725 59468 Z= 0.333 Chirality : 0.043 0.145 6728 Planarity : 0.005 0.045 7572 Dihedral : 7.067 125.542 6820 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.67 % Allowed : 10.25 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.11), residues: 5468 helix: 1.93 (0.09), residues: 3024 sheet: -0.64 (0.21), residues: 428 loop : -0.18 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1088 TYR 0.026 0.003 TYR A 917 PHE 0.028 0.003 PHE A 879 TRP 0.019 0.002 TRP B1366 HIS 0.009 0.002 HIS B 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (43732) covalent geometry : angle 0.63594 / 0.33 (59460) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.34103 / 0.21 ( 8) hydrogen bonds : bond 0.05341 / 3.56 ( 2372) hydrogen bonds : angle 4.33215 / 3.15 ( 6984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 590 time to evaluate : 1.734 Fit side-chains REVERT: A 55 LYS cc_start: 0.7244 (mttt) cc_final: 0.6902 (mppt) REVERT: A 60 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6272 (mt-10) REVERT: A 132 GLN cc_start: 0.7504 (tt0) cc_final: 0.7175 (tp-100) REVERT: A 139 ASP cc_start: 0.7129 (m-30) cc_final: 0.6867 (m-30) REVERT: A 166 LYS cc_start: 0.7640 (tttm) cc_final: 0.7269 (mptt) REVERT: A 239 MET cc_start: 0.6069 (ttm) cc_final: 0.5383 (tmm) REVERT: A 371 ASP cc_start: 0.7337 (t70) cc_final: 0.7025 (m-30) REVERT: A 381 ASN cc_start: 0.7799 (m-40) cc_final: 0.7548 (m110) REVERT: A 395 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6548 (mp0) REVERT: A 456 MET cc_start: 0.7816 (mtm) cc_final: 0.7594 (mtm) REVERT: A 464 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6573 (mt-10) REVERT: A 506 ARG cc_start: 0.7115 (ttt-90) cc_final: 0.6425 (tmm160) REVERT: A 516 GLN cc_start: 0.7047 (tt0) cc_final: 0.6772 (tm130) REVERT: A 517 ARG cc_start: 0.6444 (mtp180) cc_final: 0.6046 (mtp85) REVERT: A 521 LEU cc_start: 0.6890 (mt) cc_final: 0.6655 (mp) REVERT: A 638 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6517 (mt-10) REVERT: A 663 LYS cc_start: 0.8111 (tptm) cc_final: 0.7888 (tptm) REVERT: A 694 MET cc_start: 0.4316 (OUTLIER) cc_final: 0.4064 (ttm) REVERT: A 916 ARG cc_start: 0.8277 (tpm170) cc_final: 0.7982 (tmm-80) REVERT: A 969 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8081 (mtm-85) REVERT: A 1042 MET cc_start: 0.8517 (mtm) cc_final: 0.8150 (mmm) REVERT: A 1046 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: A 1122 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.6635 (mtm-85) REVERT: A 1128 ARG cc_start: 0.6414 (ttp80) cc_final: 0.5856 (tpp-160) REVERT: A 1151 ASP cc_start: 0.7526 (m-30) cc_final: 0.7131 (m-30) REVERT: B 55 LYS cc_start: 0.7254 (mttt) cc_final: 0.6910 (mppt) REVERT: B 60 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6287 (mt-10) REVERT: B 132 GLN cc_start: 0.7505 (tt0) cc_final: 0.7168 (tp-100) REVERT: B 139 ASP cc_start: 0.7137 (m-30) cc_final: 0.6868 (m-30) REVERT: B 166 LYS cc_start: 0.7657 (tttm) cc_final: 0.7270 (mptt) REVERT: B 239 MET cc_start: 0.6017 (ttm) cc_final: 0.5330 (tmm) REVERT: B 371 ASP cc_start: 0.7319 (t70) cc_final: 0.7006 (m-30) REVERT: B 395 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6555 (mp0) REVERT: B 456 MET cc_start: 0.7813 (mtm) cc_final: 0.7591 (mtm) REVERT: B 464 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6573 (mt-10) REVERT: B 506 ARG cc_start: 0.7104 (ttt-90) cc_final: 0.6420 (tmm160) REVERT: B 516 GLN cc_start: 0.7070 (tt0) cc_final: 0.6805 (tm130) REVERT: B 517 ARG cc_start: 0.6420 (mtp180) cc_final: 0.6023 (mtp85) REVERT: B 521 LEU cc_start: 0.6827 (mt) cc_final: 0.6571 (mp) REVERT: B 638 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6507 (mt-10) REVERT: B 663 LYS cc_start: 0.8107 (tptm) cc_final: 0.7883 (tptm) REVERT: B 694 MET cc_start: 0.4320 (OUTLIER) cc_final: 0.4069 (ttm) REVERT: B 916 ARG cc_start: 0.8297 (tpm170) cc_final: 0.7994 (tmm-80) REVERT: B 969 ARG cc_start: 0.8420 (mtm110) cc_final: 0.8077 (mtm-85) REVERT: B 1042 MET cc_start: 0.8507 (mtm) cc_final: 0.8143 (mmm) REVERT: B 1046 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: B 1122 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.6598 (mtm-85) REVERT: B 1128 ARG cc_start: 0.6343 (ttp80) cc_final: 0.5822 (tpp-160) REVERT: B 1147 MET cc_start: 0.8114 (mtm) cc_final: 0.7532 (mtm) REVERT: B 1151 ASP cc_start: 0.7503 (m-30) cc_final: 0.7076 (m-30) REVERT: C 55 LYS cc_start: 0.7253 (mttt) cc_final: 0.6909 (mppt) REVERT: C 60 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6268 (mt-10) REVERT: C 132 GLN cc_start: 0.7502 (tt0) cc_final: 0.7164 (tp-100) REVERT: C 139 ASP cc_start: 0.7129 (m-30) cc_final: 0.6861 (m-30) REVERT: C 166 LYS cc_start: 0.7662 (tttm) cc_final: 0.7282 (mptt) REVERT: C 239 MET cc_start: 0.6020 (ttm) cc_final: 0.5328 (tmm) REVERT: C 371 ASP cc_start: 0.7341 (t70) cc_final: 0.7028 (m-30) REVERT: C 395 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6547 (mp0) REVERT: C 456 MET cc_start: 0.7816 (mtm) cc_final: 0.7592 (mtm) REVERT: C 464 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6578 (mt-10) REVERT: C 506 ARG cc_start: 0.7110 (ttt-90) cc_final: 0.6417 (tmm160) REVERT: C 516 GLN cc_start: 0.7063 (tt0) cc_final: 0.6772 (tm130) REVERT: C 517 ARG cc_start: 0.6446 (mtp180) cc_final: 0.6042 (mtp85) REVERT: C 521 LEU cc_start: 0.6895 (mt) cc_final: 0.6662 (mp) REVERT: C 638 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6511 (mt-10) REVERT: C 663 LYS cc_start: 0.8109 (tptm) cc_final: 0.7883 (tptm) REVERT: C 694 MET cc_start: 0.4308 (OUTLIER) cc_final: 0.4056 (ttm) REVERT: C 916 ARG cc_start: 0.8292 (tpm170) cc_final: 0.7993 (tmm-80) REVERT: C 969 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8079 (mtm-85) REVERT: C 1042 MET cc_start: 0.8512 (mtm) cc_final: 0.8150 (mmm) REVERT: C 1046 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: C 1122 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.6795 (mtm-85) REVERT: C 1128 ARG cc_start: 0.6357 (ttp80) cc_final: 0.5833 (tpp-160) REVERT: C 1147 MET cc_start: 0.8186 (mtm) cc_final: 0.7872 (mtm) REVERT: D 55 LYS cc_start: 0.7246 (mttt) cc_final: 0.6900 (mppt) REVERT: D 60 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6281 (mt-10) REVERT: D 132 GLN cc_start: 0.7501 (tt0) cc_final: 0.7170 (tp-100) REVERT: D 139 ASP cc_start: 0.7122 (m-30) cc_final: 0.6851 (m-30) REVERT: D 166 LYS cc_start: 0.7650 (tttm) cc_final: 0.7269 (mptt) REVERT: D 239 MET cc_start: 0.6082 (ttm) cc_final: 0.5398 (tmm) REVERT: D 371 ASP cc_start: 0.7335 (t70) cc_final: 0.7031 (m-30) REVERT: D 381 ASN cc_start: 0.7809 (m-40) cc_final: 0.7568 (m110) REVERT: D 395 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6533 (mp0) REVERT: D 456 MET cc_start: 0.7815 (mtm) cc_final: 0.7591 (mtm) REVERT: D 464 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 506 ARG cc_start: 0.7106 (ttt-90) cc_final: 0.6421 (tmm160) REVERT: D 516 GLN cc_start: 0.7060 (tt0) cc_final: 0.6794 (tm130) REVERT: D 517 ARG cc_start: 0.6443 (mtp180) cc_final: 0.6038 (mtp85) REVERT: D 521 LEU cc_start: 0.6891 (mt) cc_final: 0.6658 (mp) REVERT: D 638 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6507 (mt-10) REVERT: D 663 LYS cc_start: 0.8103 (tptm) cc_final: 0.7879 (tptm) REVERT: D 694 MET cc_start: 0.4314 (OUTLIER) cc_final: 0.4060 (ttm) REVERT: D 916 ARG cc_start: 0.8287 (tpm170) cc_final: 0.7985 (tmm-80) REVERT: D 969 ARG cc_start: 0.8420 (mtm110) cc_final: 0.8076 (mtm-85) REVERT: D 1042 MET cc_start: 0.8508 (mtm) cc_final: 0.8147 (mmm) REVERT: D 1046 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: D 1122 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.6792 (mtm-85) REVERT: D 1128 ARG cc_start: 0.6351 (ttp80) cc_final: 0.5828 (tpp-160) REVERT: D 1147 MET cc_start: 0.8111 (mtm) cc_final: 0.7875 (mtm) REVERT: D 1151 ASP cc_start: 0.7561 (m-30) cc_final: 0.7302 (m-30) outliers start: 114 outliers final: 61 residues processed: 645 average time/residue: 0.8295 time to fit residues: 647.0904 Evaluate side-chains 633 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 564 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1401 MET Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1401 MET Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 931 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1401 MET Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 931 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1401 MET Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 491 optimal weight: 5.9990 chunk 527 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 481 optimal weight: 0.7980 chunk 373 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 499 optimal weight: 0.9980 chunk 384 optimal weight: 1.9990 chunk 360 optimal weight: 0.8980 chunk 483 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN A1129 GLN A1156 HIS B 696 ASN C 696 ASN D 696 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140105 restraints weight = 41514.170| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.37 r_work: 0.3332 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43736 Z= 0.127 Angle : 0.509 6.370 59468 Z= 0.267 Chirality : 0.038 0.139 6728 Planarity : 0.004 0.041 7572 Dihedral : 6.782 124.390 6820 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.85 % Allowed : 11.63 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.11), residues: 5468 helix: 2.21 (0.09), residues: 3032 sheet: -0.67 (0.22), residues: 428 loop : -0.08 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 341 TYR 0.017 0.002 TYR C1063 PHE 0.020 0.002 PHE C 879 TRP 0.014 0.002 TRP B1366 HIS 0.006 0.001 HIS C 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (43732) covalent geometry : angle 0.50918 / 0.27 (59460) SS BOND : bond 0.00007 / 0.00 ( 4) SS BOND : angle 0.29533 / 0.18 ( 8) hydrogen bonds : bond 0.04327 / 2.88 ( 2372) hydrogen bonds : angle 4.02002 / 2.92 ( 6984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 574 time to evaluate : 1.582 Fit side-chains REVERT: A 55 LYS cc_start: 0.7229 (mttt) cc_final: 0.6891 (mppt) REVERT: A 60 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6249 (mt-10) REVERT: A 132 GLN cc_start: 0.7493 (tt0) cc_final: 0.7171 (tp-100) REVERT: A 139 ASP cc_start: 0.7132 (m-30) cc_final: 0.6860 (m-30) REVERT: A 166 LYS cc_start: 0.7634 (tttm) cc_final: 0.7207 (mptp) REVERT: A 239 MET cc_start: 0.6074 (ttm) cc_final: 0.5388 (tmm) REVERT: A 371 ASP cc_start: 0.7314 (t70) cc_final: 0.7038 (m-30) REVERT: A 381 ASN cc_start: 0.7776 (m-40) cc_final: 0.7528 (m110) REVERT: A 395 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6582 (mp0) REVERT: A 456 MET cc_start: 0.7807 (mtm) cc_final: 0.7569 (mtm) REVERT: A 464 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6520 (mt-10) REVERT: A 506 ARG cc_start: 0.7104 (ttt-90) cc_final: 0.6401 (tmm160) REVERT: A 516 GLN cc_start: 0.7064 (tt0) cc_final: 0.6785 (tm130) REVERT: A 517 ARG cc_start: 0.6395 (mtp180) cc_final: 0.5992 (mtp85) REVERT: A 521 LEU cc_start: 0.6907 (mt) cc_final: 0.6653 (mp) REVERT: A 638 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6532 (mt-10) REVERT: A 659 GLN cc_start: 0.7274 (mt0) cc_final: 0.6731 (mt0) REVERT: A 663 LYS cc_start: 0.8132 (tptm) cc_final: 0.7765 (mtpt) REVERT: A 667 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 694 MET cc_start: 0.4070 (ttp) cc_final: 0.3831 (ttm) REVERT: A 916 ARG cc_start: 0.8227 (tpm170) cc_final: 0.7946 (tmm-80) REVERT: A 969 ARG cc_start: 0.8384 (mtm110) cc_final: 0.8068 (mtm-85) REVERT: A 1042 MET cc_start: 0.8621 (mtm) cc_final: 0.8292 (mmm) REVERT: A 1046 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 1122 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7067 (mtp180) REVERT: A 1128 ARG cc_start: 0.6298 (ttp80) cc_final: 0.5753 (tpt-90) REVERT: A 1147 MET cc_start: 0.8026 (mtm) cc_final: 0.7533 (mtm) REVERT: A 1151 ASP cc_start: 0.7533 (m-30) cc_final: 0.7147 (m-30) REVERT: B 55 LYS cc_start: 0.7231 (mttt) cc_final: 0.6892 (mppt) REVERT: B 60 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6278 (mt-10) REVERT: B 132 GLN cc_start: 0.7500 (tt0) cc_final: 0.7196 (tp-100) REVERT: B 139 ASP cc_start: 0.7144 (m-30) cc_final: 0.6864 (m-30) REVERT: B 166 LYS cc_start: 0.7633 (tttm) cc_final: 0.7206 (mptp) REVERT: B 239 MET cc_start: 0.6054 (ttm) cc_final: 0.5370 (tmm) REVERT: B 371 ASP cc_start: 0.7324 (t70) cc_final: 0.7064 (m-30) REVERT: B 395 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6595 (mp0) REVERT: B 456 MET cc_start: 0.7807 (mtm) cc_final: 0.7567 (mtm) REVERT: B 464 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6505 (mt-10) REVERT: B 506 ARG cc_start: 0.7098 (ttt-90) cc_final: 0.6407 (tmm160) REVERT: B 516 GLN cc_start: 0.7053 (tt0) cc_final: 0.6777 (tm130) REVERT: B 517 ARG cc_start: 0.6415 (mtp180) cc_final: 0.6000 (mtp85) REVERT: B 521 LEU cc_start: 0.6814 (mt) cc_final: 0.6555 (mp) REVERT: B 638 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6518 (mt-10) REVERT: B 659 GLN cc_start: 0.7260 (mt0) cc_final: 0.6716 (mt0) REVERT: B 663 LYS cc_start: 0.8132 (tptm) cc_final: 0.7761 (mtpt) REVERT: B 667 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 694 MET cc_start: 0.4068 (ttp) cc_final: 0.3816 (ttm) REVERT: B 916 ARG cc_start: 0.8231 (tpm170) cc_final: 0.7951 (tmm-80) REVERT: B 969 ARG cc_start: 0.8388 (mtm110) cc_final: 0.8072 (mtm-85) REVERT: B 1042 MET cc_start: 0.8599 (mtm) cc_final: 0.8269 (mmm) REVERT: B 1046 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 1122 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6596 (mtm-85) REVERT: B 1128 ARG cc_start: 0.6325 (ttp80) cc_final: 0.5797 (tpt-90) REVERT: B 1147 MET cc_start: 0.8090 (mtm) cc_final: 0.7581 (mtm) REVERT: B 1151 ASP cc_start: 0.7543 (m-30) cc_final: 0.7116 (m-30) REVERT: B 1207 HIS cc_start: 0.7113 (m90) cc_final: 0.6899 (m-70) REVERT: C 55 LYS cc_start: 0.7236 (mttt) cc_final: 0.6896 (mppt) REVERT: C 60 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6273 (mt-10) REVERT: C 132 GLN cc_start: 0.7501 (tt0) cc_final: 0.7193 (tp-100) REVERT: C 139 ASP cc_start: 0.7142 (m-30) cc_final: 0.6862 (m-30) REVERT: C 166 LYS cc_start: 0.7639 (tttm) cc_final: 0.7214 (mptp) REVERT: C 239 MET cc_start: 0.6085 (ttm) cc_final: 0.5396 (tmm) REVERT: C 371 ASP cc_start: 0.7333 (t70) cc_final: 0.7073 (m-30) REVERT: C 381 ASN cc_start: 0.7784 (m-40) cc_final: 0.7537 (m110) REVERT: C 395 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6590 (mp0) REVERT: C 456 MET cc_start: 0.7805 (mtm) cc_final: 0.7568 (mtm) REVERT: C 464 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6544 (mt-10) REVERT: C 506 ARG cc_start: 0.7099 (ttt-90) cc_final: 0.6397 (tmm160) REVERT: C 516 GLN cc_start: 0.7044 (tt0) cc_final: 0.6765 (tm130) REVERT: C 517 ARG cc_start: 0.6405 (mtp180) cc_final: 0.5991 (mtp85) REVERT: C 521 LEU cc_start: 0.6909 (mt) cc_final: 0.6651 (mp) REVERT: C 638 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6527 (mt-10) REVERT: C 659 GLN cc_start: 0.7259 (mt0) cc_final: 0.6713 (mt0) REVERT: C 663 LYS cc_start: 0.8134 (tptm) cc_final: 0.7762 (mtpt) REVERT: C 667 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: C 694 MET cc_start: 0.4069 (ttp) cc_final: 0.3820 (ttm) REVERT: C 916 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7948 (tmm-80) REVERT: C 969 ARG cc_start: 0.8384 (mtm110) cc_final: 0.8069 (mtm-85) REVERT: C 1042 MET cc_start: 0.8619 (mtm) cc_final: 0.8291 (mmm) REVERT: C 1046 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: C 1122 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6603 (mtm-85) REVERT: C 1128 ARG cc_start: 0.6325 (ttp80) cc_final: 0.5800 (tpt-90) REVERT: C 1147 MET cc_start: 0.8152 (mtm) cc_final: 0.7662 (mtm) REVERT: C 1151 ASP cc_start: 0.7721 (m-30) cc_final: 0.7442 (m-30) REVERT: C 1207 HIS cc_start: 0.7106 (m90) cc_final: 0.6893 (m-70) REVERT: D 55 LYS cc_start: 0.7228 (mttt) cc_final: 0.6885 (mppt) REVERT: D 60 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6265 (mt-10) REVERT: D 132 GLN cc_start: 0.7490 (tt0) cc_final: 0.7191 (tp-100) REVERT: D 139 ASP cc_start: 0.7132 (m-30) cc_final: 0.6854 (m-30) REVERT: D 166 LYS cc_start: 0.7638 (tttm) cc_final: 0.7216 (mptp) REVERT: D 239 MET cc_start: 0.6079 (ttm) cc_final: 0.5392 (tmm) REVERT: D 371 ASP cc_start: 0.7307 (t70) cc_final: 0.7037 (m-30) REVERT: D 395 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6586 (mp0) REVERT: D 456 MET cc_start: 0.7810 (mtm) cc_final: 0.7572 (mtm) REVERT: D 464 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6535 (mt-10) REVERT: D 506 ARG cc_start: 0.7097 (ttt-90) cc_final: 0.6406 (tmm160) REVERT: D 516 GLN cc_start: 0.7044 (tt0) cc_final: 0.6766 (tm130) REVERT: D 517 ARG cc_start: 0.6404 (mtp180) cc_final: 0.5990 (mtp85) REVERT: D 521 LEU cc_start: 0.6903 (mt) cc_final: 0.6647 (mp) REVERT: D 638 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6516 (mt-10) REVERT: D 659 GLN cc_start: 0.7271 (mt0) cc_final: 0.6729 (mt0) REVERT: D 663 LYS cc_start: 0.8134 (tptm) cc_final: 0.7763 (mtpt) REVERT: D 667 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: D 694 MET cc_start: 0.4060 (ttp) cc_final: 0.3813 (ttm) REVERT: D 916 ARG cc_start: 0.8223 (tpm170) cc_final: 0.7944 (tmm-80) REVERT: D 969 ARG cc_start: 0.8380 (mtm110) cc_final: 0.8065 (mtm-85) REVERT: D 1042 MET cc_start: 0.8613 (mtm) cc_final: 0.8287 (mmm) REVERT: D 1046 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: D 1122 ARG cc_start: 0.7289 (mtm-85) cc_final: 0.6593 (mtm-85) REVERT: D 1128 ARG cc_start: 0.6330 (ttp80) cc_final: 0.5804 (tpt-90) REVERT: D 1147 MET cc_start: 0.8051 (mtm) cc_final: 0.7524 (mtm) REVERT: D 1151 ASP cc_start: 0.7544 (m-30) cc_final: 0.7137 (m-30) REVERT: D 1207 HIS cc_start: 0.7104 (m90) cc_final: 0.6875 (m-70) outliers start: 79 outliers final: 40 residues processed: 613 average time/residue: 0.7604 time to fit residues: 563.5032 Evaluate side-chains 616 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 568 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1230 LYS Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1230 LYS Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 418 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 475 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 460 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS A 696 ASN A1080 HIS B 457 HIS B 696 ASN C 457 HIS C 696 ASN D 457 HIS D 696 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137488 restraints weight = 41491.557| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.29 r_work: 0.3297 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 43736 Z= 0.230 Angle : 0.647 8.754 59468 Z= 0.338 Chirality : 0.043 0.145 6728 Planarity : 0.005 0.044 7572 Dihedral : 7.013 125.324 6820 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.88 % Allowed : 11.59 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.11), residues: 5468 helix: 1.92 (0.09), residues: 3028 sheet: -0.66 (0.22), residues: 428 loop : -0.23 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1088 TYR 0.027 0.003 TYR D 917 PHE 0.029 0.003 PHE B 879 TRP 0.019 0.003 TRP A1366 HIS 0.011 0.002 HIS A 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (43732) covalent geometry : angle 0.64715 / 0.34 (59460) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.40082 / 0.24 ( 8) hydrogen bonds : bond 0.05403 / 3.60 ( 2372) hydrogen bonds : angle 4.33050 / 3.15 ( 6984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 571 time to evaluate : 1.401 Fit side-chains REVERT: A 55 LYS cc_start: 0.7219 (mttt) cc_final: 0.6926 (mppt) REVERT: A 60 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6305 (mt-10) REVERT: A 132 GLN cc_start: 0.7548 (tt0) cc_final: 0.7087 (tp-100) REVERT: A 139 ASP cc_start: 0.7138 (m-30) cc_final: 0.6876 (m-30) REVERT: A 166 LYS cc_start: 0.7694 (tttm) cc_final: 0.7269 (mptt) REVERT: A 239 MET cc_start: 0.6078 (ttm) cc_final: 0.5515 (tmm) REVERT: A 371 ASP cc_start: 0.7359 (t70) cc_final: 0.7058 (m-30) REVERT: A 381 ASN cc_start: 0.7804 (m-40) cc_final: 0.7557 (m110) REVERT: A 395 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6559 (mp0) REVERT: A 447 ILE cc_start: 0.6489 (tt) cc_final: 0.5873 (pp) REVERT: A 464 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6579 (mt-10) REVERT: A 506 ARG cc_start: 0.7152 (ttt-90) cc_final: 0.6460 (tmm160) REVERT: A 516 GLN cc_start: 0.7098 (tt0) cc_final: 0.6819 (tm130) REVERT: A 517 ARG cc_start: 0.6427 (mtp180) cc_final: 0.6044 (mtp85) REVERT: A 521 LEU cc_start: 0.6865 (mt) cc_final: 0.6620 (mp) REVERT: A 575 ASN cc_start: 0.6125 (m-40) cc_final: 0.5738 (m-40) REVERT: A 663 LYS cc_start: 0.8150 (tptm) cc_final: 0.7843 (ttmt) REVERT: A 694 MET cc_start: 0.4122 (ttp) cc_final: 0.3902 (ttm) REVERT: A 916 ARG cc_start: 0.8304 (tpm170) cc_final: 0.8051 (tmm-80) REVERT: A 969 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8109 (mtm-85) REVERT: A 1042 MET cc_start: 0.8515 (mtm) cc_final: 0.8179 (mmm) REVERT: A 1046 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: A 1122 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.6758 (mtm-85) REVERT: A 1128 ARG cc_start: 0.6342 (ttp80) cc_final: 0.5817 (tpp-160) REVERT: A 1147 MET cc_start: 0.8171 (mtm) cc_final: 0.7971 (mtm) REVERT: A 1150 MET cc_start: 0.7634 (tpp) cc_final: 0.7104 (mtt) REVERT: A 1151 ASP cc_start: 0.7539 (m-30) cc_final: 0.7314 (m-30) REVERT: A 1157 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7312 (mtt) REVERT: A 1252 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: B 55 LYS cc_start: 0.7230 (mttt) cc_final: 0.6938 (mppt) REVERT: B 60 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6332 (mt-10) REVERT: B 132 GLN cc_start: 0.7565 (tt0) cc_final: 0.7093 (tp-100) REVERT: B 139 ASP cc_start: 0.7141 (m-30) cc_final: 0.6878 (m-30) REVERT: B 166 LYS cc_start: 0.7690 (tttm) cc_final: 0.7274 (mptt) REVERT: B 239 MET cc_start: 0.6093 (ttm) cc_final: 0.5527 (tmm) REVERT: B 371 ASP cc_start: 0.7358 (t70) cc_final: 0.7060 (m-30) REVERT: B 381 ASN cc_start: 0.7806 (m-40) cc_final: 0.7560 (m110) REVERT: B 395 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6586 (mp0) REVERT: B 447 ILE cc_start: 0.6499 (tt) cc_final: 0.5866 (pp) REVERT: B 464 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6584 (mt-10) REVERT: B 506 ARG cc_start: 0.7150 (ttt-90) cc_final: 0.6465 (tmm160) REVERT: B 516 GLN cc_start: 0.7096 (tt0) cc_final: 0.6822 (tm130) REVERT: B 517 ARG cc_start: 0.6467 (mtp180) cc_final: 0.6074 (mtp85) REVERT: B 521 LEU cc_start: 0.6820 (mt) cc_final: 0.6549 (mp) REVERT: B 575 ASN cc_start: 0.6113 (m-40) cc_final: 0.5728 (m-40) REVERT: B 663 LYS cc_start: 0.8148 (tptm) cc_final: 0.7837 (ttmt) REVERT: B 694 MET cc_start: 0.4120 (ttp) cc_final: 0.3885 (ttm) REVERT: B 916 ARG cc_start: 0.8304 (tpm170) cc_final: 0.8054 (tmm-80) REVERT: B 969 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8107 (mtm-85) REVERT: B 1042 MET cc_start: 0.8510 (mtm) cc_final: 0.8176 (mmm) REVERT: B 1046 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: B 1122 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6743 (mtm-85) REVERT: B 1128 ARG cc_start: 0.6326 (ttp80) cc_final: 0.5812 (tpp-160) REVERT: B 1147 MET cc_start: 0.8158 (mtm) cc_final: 0.7753 (mtm) REVERT: B 1151 ASP cc_start: 0.7495 (m-30) cc_final: 0.7109 (m-30) REVERT: B 1252 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: C 55 LYS cc_start: 0.7222 (mttt) cc_final: 0.6926 (mppt) REVERT: C 60 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6324 (mt-10) REVERT: C 132 GLN cc_start: 0.7559 (tt0) cc_final: 0.7085 (tp-100) REVERT: C 139 ASP cc_start: 0.7130 (m-30) cc_final: 0.6865 (m-30) REVERT: C 166 LYS cc_start: 0.7701 (tttm) cc_final: 0.7293 (mptt) REVERT: C 239 MET cc_start: 0.6093 (ttm) cc_final: 0.5525 (tmm) REVERT: C 371 ASP cc_start: 0.7353 (t70) cc_final: 0.7041 (m-30) REVERT: C 381 ASN cc_start: 0.7805 (m-40) cc_final: 0.7558 (m110) REVERT: C 395 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6587 (mp0) REVERT: C 447 ILE cc_start: 0.6506 (tt) cc_final: 0.5876 (pp) REVERT: C 464 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6580 (mt-10) REVERT: C 506 ARG cc_start: 0.7155 (ttt-90) cc_final: 0.6463 (tmm160) REVERT: C 516 GLN cc_start: 0.7095 (tt0) cc_final: 0.6812 (tm130) REVERT: C 517 ARG cc_start: 0.6423 (mtp180) cc_final: 0.6047 (mtp85) REVERT: C 521 LEU cc_start: 0.6862 (mt) cc_final: 0.6632 (mp) REVERT: C 575 ASN cc_start: 0.6133 (m-40) cc_final: 0.5744 (m-40) REVERT: C 663 LYS cc_start: 0.8152 (tptm) cc_final: 0.7838 (ttmt) REVERT: C 694 MET cc_start: 0.4118 (ttp) cc_final: 0.3901 (ttm) REVERT: C 916 ARG cc_start: 0.8302 (tpm170) cc_final: 0.8053 (tmm-80) REVERT: C 969 ARG cc_start: 0.8430 (mtm110) cc_final: 0.8106 (mtm-85) REVERT: C 1042 MET cc_start: 0.8514 (mtm) cc_final: 0.8177 (mmm) REVERT: C 1046 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: C 1122 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.6761 (mtm-85) REVERT: C 1128 ARG cc_start: 0.6326 (ttp80) cc_final: 0.5811 (tpp-160) REVERT: C 1147 MET cc_start: 0.8234 (mtm) cc_final: 0.7779 (mtm) REVERT: C 1151 ASP cc_start: 0.7817 (m-30) cc_final: 0.7506 (m-30) REVERT: C 1252 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: D 55 LYS cc_start: 0.7172 (mttt) cc_final: 0.6894 (mppt) REVERT: D 60 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6311 (mt-10) REVERT: D 132 GLN cc_start: 0.7547 (tt0) cc_final: 0.7084 (tp-100) REVERT: D 139 ASP cc_start: 0.7121 (m-30) cc_final: 0.6858 (m-30) REVERT: D 166 LYS cc_start: 0.7690 (tttm) cc_final: 0.7263 (mptt) REVERT: D 239 MET cc_start: 0.6086 (ttm) cc_final: 0.5523 (tmm) REVERT: D 371 ASP cc_start: 0.7361 (t70) cc_final: 0.7058 (m-30) REVERT: D 381 ASN cc_start: 0.7795 (m-40) cc_final: 0.7548 (m110) REVERT: D 395 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6581 (mp0) REVERT: D 447 ILE cc_start: 0.6501 (tt) cc_final: 0.5867 (pp) REVERT: D 464 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6587 (mt-10) REVERT: D 506 ARG cc_start: 0.7150 (ttt-90) cc_final: 0.6461 (tmm160) REVERT: D 516 GLN cc_start: 0.7074 (tt0) cc_final: 0.6795 (tm130) REVERT: D 517 ARG cc_start: 0.6416 (mtp180) cc_final: 0.6030 (mtp85) REVERT: D 521 LEU cc_start: 0.6859 (mt) cc_final: 0.6612 (mp) REVERT: D 575 ASN cc_start: 0.6112 (m-40) cc_final: 0.5725 (m-40) REVERT: D 663 LYS cc_start: 0.8149 (tptm) cc_final: 0.7840 (mptp) REVERT: D 694 MET cc_start: 0.4120 (ttp) cc_final: 0.3903 (ttm) REVERT: D 916 ARG cc_start: 0.8294 (tpm170) cc_final: 0.8047 (tmm-80) REVERT: D 969 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8106 (mtm-85) REVERT: D 1042 MET cc_start: 0.8512 (mtm) cc_final: 0.8178 (mmm) REVERT: D 1046 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: D 1122 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6727 (mtm-85) REVERT: D 1128 ARG cc_start: 0.6340 (ttp80) cc_final: 0.5822 (tpp-160) REVERT: D 1147 MET cc_start: 0.8145 (mtm) cc_final: 0.7736 (mtm) REVERT: D 1151 ASP cc_start: 0.7586 (m-30) cc_final: 0.7188 (m-30) REVERT: D 1252 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7320 (tp30) outliers start: 80 outliers final: 56 residues processed: 611 average time/residue: 0.6701 time to fit residues: 495.6498 Evaluate side-chains 627 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 562 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1230 LYS Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1230 LYS Chi-restraints excluded: chain B residue 1252 GLU Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 931 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1230 LYS Chi-restraints excluded: chain C residue 1252 GLU Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 931 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1230 LYS Chi-restraints excluded: chain D residue 1252 GLU Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 362 optimal weight: 2.9990 chunk 473 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 455 optimal weight: 0.0570 chunk 505 optimal weight: 0.5980 chunk 220 optimal weight: 0.9990 chunk 501 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 346 optimal weight: 0.6980 chunk 487 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN C 696 ASN D 696 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.174149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.140293 restraints weight = 41729.579| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.35 r_work: 0.3335 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43736 Z= 0.115 Angle : 0.506 7.240 59468 Z= 0.263 Chirality : 0.038 0.138 6728 Planarity : 0.003 0.040 7572 Dihedral : 6.703 124.234 6820 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.38 % Allowed : 12.29 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.11), residues: 5468 helix: 2.24 (0.09), residues: 3036 sheet: -0.68 (0.22), residues: 428 loop : -0.10 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.018 0.001 TYR C1063 PHE 0.018 0.002 PHE D 879 TRP 0.014 0.002 TRP A1366 HIS 0.006 0.001 HIS D 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (43732) covalent geometry : angle 0.50610 / 0.26 (59460) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 0.27884 / 0.16 ( 8) hydrogen bonds : bond 0.04194 / 2.79 ( 2372) hydrogen bonds : angle 3.98757 / 2.90 ( 6984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 576 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7185 (mttt) cc_final: 0.6883 (mppt) REVERT: A 60 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6254 (mt-10) REVERT: A 132 GLN cc_start: 0.7496 (tt0) cc_final: 0.7209 (tp-100) REVERT: A 139 ASP cc_start: 0.7188 (m-30) cc_final: 0.6932 (m-30) REVERT: A 166 LYS cc_start: 0.7622 (tttm) cc_final: 0.7180 (mptp) REVERT: A 239 MET cc_start: 0.6034 (ttm) cc_final: 0.5460 (tmm) REVERT: A 371 ASP cc_start: 0.7339 (t70) cc_final: 0.6998 (m-30) REVERT: A 381 ASN cc_start: 0.7831 (m-40) cc_final: 0.7581 (m110) REVERT: A 395 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6573 (mp0) REVERT: A 456 MET cc_start: 0.7782 (mtm) cc_final: 0.7554 (mtm) REVERT: A 464 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6550 (mt-10) REVERT: A 516 GLN cc_start: 0.7006 (tt0) cc_final: 0.6735 (tm130) REVERT: A 517 ARG cc_start: 0.6379 (mtp180) cc_final: 0.5972 (mtp85) REVERT: A 521 LEU cc_start: 0.6878 (mt) cc_final: 0.6608 (mp) REVERT: A 659 GLN cc_start: 0.7308 (mt0) cc_final: 0.6789 (mt0) REVERT: A 663 LYS cc_start: 0.8112 (tptm) cc_final: 0.7757 (mtpt) REVERT: A 667 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: A 694 MET cc_start: 0.4160 (ttp) cc_final: 0.3948 (ttm) REVERT: A 916 ARG cc_start: 0.8220 (tpm170) cc_final: 0.7937 (tmm-80) REVERT: A 969 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8086 (mtm-85) REVERT: A 1042 MET cc_start: 0.8597 (mtm) cc_final: 0.8271 (mmm) REVERT: A 1046 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 1122 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: A 1128 ARG cc_start: 0.6321 (ttp80) cc_final: 0.5759 (tpt-90) REVERT: A 1150 MET cc_start: 0.7622 (tpp) cc_final: 0.7386 (mtt) REVERT: A 1151 ASP cc_start: 0.7492 (m-30) cc_final: 0.7255 (m-30) REVERT: A 1157 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7202 (mtt) REVERT: B 55 LYS cc_start: 0.7186 (mttt) cc_final: 0.6885 (mppt) REVERT: B 60 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6261 (mt-10) REVERT: B 132 GLN cc_start: 0.7539 (tt0) cc_final: 0.7130 (tp-100) REVERT: B 139 ASP cc_start: 0.7199 (m-30) cc_final: 0.6942 (m-30) REVERT: B 166 LYS cc_start: 0.7626 (tttm) cc_final: 0.7175 (mptp) REVERT: B 239 MET cc_start: 0.6022 (ttm) cc_final: 0.5452 (tmm) REVERT: B 371 ASP cc_start: 0.7399 (t70) cc_final: 0.7055 (m-30) REVERT: B 395 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6580 (mp0) REVERT: B 456 MET cc_start: 0.7779 (mtm) cc_final: 0.7550 (mtm) REVERT: B 464 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6543 (mt-10) REVERT: B 516 GLN cc_start: 0.7038 (tt0) cc_final: 0.6770 (tm130) REVERT: B 517 ARG cc_start: 0.6379 (mtp180) cc_final: 0.5974 (mtp85) REVERT: B 521 LEU cc_start: 0.6767 (mt) cc_final: 0.6510 (mp) REVERT: B 659 GLN cc_start: 0.7299 (mt0) cc_final: 0.6778 (mt0) REVERT: B 663 LYS cc_start: 0.8115 (tptm) cc_final: 0.7760 (mtpt) REVERT: B 667 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: B 694 MET cc_start: 0.4156 (ttp) cc_final: 0.3944 (ttm) REVERT: B 916 ARG cc_start: 0.8222 (tpm170) cc_final: 0.7941 (tmm-80) REVERT: B 969 ARG cc_start: 0.8404 (mtm110) cc_final: 0.8085 (mtm-85) REVERT: B 1042 MET cc_start: 0.8598 (mtm) cc_final: 0.8269 (mmm) REVERT: B 1046 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: B 1122 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.7060 (mtm-85) REVERT: B 1128 ARG cc_start: 0.6307 (ttp80) cc_final: 0.5737 (tpt-90) REVERT: B 1151 ASP cc_start: 0.7520 (m-30) cc_final: 0.7252 (m-30) REVERT: B 1207 HIS cc_start: 0.7076 (m90) cc_final: 0.6856 (m-70) REVERT: C 55 LYS cc_start: 0.7177 (mttt) cc_final: 0.6873 (mppt) REVERT: C 60 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6235 (mt-10) REVERT: C 132 GLN cc_start: 0.7533 (tt0) cc_final: 0.7131 (tp-100) REVERT: C 139 ASP cc_start: 0.7190 (m-30) cc_final: 0.6931 (m-30) REVERT: C 166 LYS cc_start: 0.7637 (tttm) cc_final: 0.7193 (mptp) REVERT: C 239 MET cc_start: 0.6045 (ttm) cc_final: 0.5478 (tmm) REVERT: C 371 ASP cc_start: 0.7390 (t70) cc_final: 0.7051 (m-30) REVERT: C 395 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6582 (mp0) REVERT: C 456 MET cc_start: 0.7785 (mtm) cc_final: 0.7556 (mtm) REVERT: C 464 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6549 (mt-10) REVERT: C 516 GLN cc_start: 0.7010 (tt0) cc_final: 0.6732 (tm130) REVERT: C 517 ARG cc_start: 0.6372 (mtp180) cc_final: 0.5962 (mtp85) REVERT: C 521 LEU cc_start: 0.6873 (mt) cc_final: 0.6599 (mp) REVERT: C 659 GLN cc_start: 0.7301 (mt0) cc_final: 0.6782 (mt0) REVERT: C 663 LYS cc_start: 0.8123 (tptm) cc_final: 0.7766 (mtpt) REVERT: C 667 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: C 694 MET cc_start: 0.4153 (ttp) cc_final: 0.3943 (ttm) REVERT: C 916 ARG cc_start: 0.8221 (tpm170) cc_final: 0.7941 (tmm-80) REVERT: C 969 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8091 (mtm-85) REVERT: C 1042 MET cc_start: 0.8622 (mtm) cc_final: 0.8287 (mmm) REVERT: C 1046 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: C 1122 ARG cc_start: 0.7299 (mtm-85) cc_final: 0.7050 (mtm-85) REVERT: C 1128 ARG cc_start: 0.6316 (ttp80) cc_final: 0.5763 (tpt-90) REVERT: C 1147 MET cc_start: 0.8127 (mtm) cc_final: 0.7671 (mtm) REVERT: C 1151 ASP cc_start: 0.7691 (m-30) cc_final: 0.7405 (m-30) REVERT: C 1207 HIS cc_start: 0.7071 (m90) cc_final: 0.6855 (m-70) REVERT: D 55 LYS cc_start: 0.7183 (mttt) cc_final: 0.6881 (mppt) REVERT: D 60 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6247 (mt-10) REVERT: D 132 GLN cc_start: 0.7513 (tt0) cc_final: 0.7123 (tp-100) REVERT: D 139 ASP cc_start: 0.7186 (m-30) cc_final: 0.6928 (m-30) REVERT: D 166 LYS cc_start: 0.7615 (tttm) cc_final: 0.7178 (mptp) REVERT: D 239 MET cc_start: 0.6047 (ttm) cc_final: 0.5474 (tmm) REVERT: D 371 ASP cc_start: 0.7336 (t70) cc_final: 0.7008 (m-30) REVERT: D 381 ASN cc_start: 0.7823 (m-40) cc_final: 0.7572 (m110) REVERT: D 395 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6576 (mp0) REVERT: D 456 MET cc_start: 0.7785 (mtm) cc_final: 0.7557 (mtm) REVERT: D 464 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6545 (mt-10) REVERT: D 516 GLN cc_start: 0.7012 (tt0) cc_final: 0.6738 (tm130) REVERT: D 517 ARG cc_start: 0.6395 (mtp180) cc_final: 0.5990 (mtp85) REVERT: D 521 LEU cc_start: 0.6873 (mt) cc_final: 0.6599 (mp) REVERT: D 659 GLN cc_start: 0.7310 (mt0) cc_final: 0.6792 (mt0) REVERT: D 663 LYS cc_start: 0.8113 (tptm) cc_final: 0.7758 (mtpt) REVERT: D 667 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: D 694 MET cc_start: 0.4149 (ttp) cc_final: 0.3935 (ttm) REVERT: D 916 ARG cc_start: 0.8217 (tpm170) cc_final: 0.7935 (tmm-80) REVERT: D 969 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8088 (mtm-85) REVERT: D 1042 MET cc_start: 0.8597 (mtm) cc_final: 0.8268 (mmm) REVERT: D 1046 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: D 1122 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.7042 (mtm-85) REVERT: D 1128 ARG cc_start: 0.6316 (ttp80) cc_final: 0.5756 (tpt-90) REVERT: D 1147 MET cc_start: 0.8069 (mtm) cc_final: 0.7644 (mtm) REVERT: D 1151 ASP cc_start: 0.7564 (m-30) cc_final: 0.7131 (m-30) REVERT: D 1207 HIS cc_start: 0.7077 (m90) cc_final: 0.6861 (m-70) outliers start: 59 outliers final: 40 residues processed: 611 average time/residue: 0.5093 time to fit residues: 377.5278 Evaluate side-chains 613 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 564 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1230 LYS Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1230 LYS Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1230 LYS Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 347 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 518 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 chunk 440 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN C 696 ASN D 696 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140193 restraints weight = 41954.422| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.35 r_work: 0.3334 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 43736 Z= 0.121 Angle : 0.512 7.921 59468 Z= 0.266 Chirality : 0.038 0.163 6728 Planarity : 0.004 0.040 7572 Dihedral : 6.591 124.156 6820 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.38 % Allowed : 12.12 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.11), residues: 5468 helix: 2.32 (0.09), residues: 3036 sheet: -0.69 (0.22), residues: 428 loop : -0.08 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 341 TYR 0.018 0.002 TYR C1063 PHE 0.020 0.002 PHE D 879 TRP 0.015 0.002 TRP A1366 HIS 0.006 0.001 HIS B 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (43732) covalent geometry : angle 0.51182 / 0.27 (59460) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 0.25210 / 0.15 ( 8) hydrogen bonds : bond 0.04217 / 2.81 ( 2372) hydrogen bonds : angle 3.95817 / 2.88 ( 6984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 553 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7173 (mttt) cc_final: 0.6881 (mppt) REVERT: A 60 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6199 (mt-10) REVERT: A 132 GLN cc_start: 0.7416 (tt0) cc_final: 0.7155 (tp-100) REVERT: A 139 ASP cc_start: 0.7162 (m-30) cc_final: 0.6884 (m-30) REVERT: A 166 LYS cc_start: 0.7578 (tttm) cc_final: 0.7125 (mptp) REVERT: A 371 ASP cc_start: 0.7348 (t70) cc_final: 0.7026 (m-30) REVERT: A 381 ASN cc_start: 0.7799 (m-40) cc_final: 0.7548 (m110) REVERT: A 395 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6524 (mp0) REVERT: A 456 MET cc_start: 0.7771 (mtm) cc_final: 0.7541 (mtm) REVERT: A 464 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6439 (mt-10) REVERT: A 516 GLN cc_start: 0.6961 (tt0) cc_final: 0.6694 (tm130) REVERT: A 517 ARG cc_start: 0.6337 (mtp180) cc_final: 0.5945 (mtp85) REVERT: A 521 LEU cc_start: 0.6818 (mt) cc_final: 0.6564 (mp) REVERT: A 659 GLN cc_start: 0.7269 (mt0) cc_final: 0.6755 (mt0) REVERT: A 663 LYS cc_start: 0.8077 (tptm) cc_final: 0.7727 (mtpt) REVERT: A 667 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 694 MET cc_start: 0.4222 (ttp) cc_final: 0.4005 (ttm) REVERT: A 854 MET cc_start: 0.6899 (ttm) cc_final: 0.6675 (ttp) REVERT: A 916 ARG cc_start: 0.8203 (tpm170) cc_final: 0.7923 (tmm-80) REVERT: A 931 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: A 969 ARG cc_start: 0.8362 (mtm110) cc_final: 0.8068 (mtm-85) REVERT: A 1042 MET cc_start: 0.8549 (mtm) cc_final: 0.8208 (mmm) REVERT: A 1046 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: A 1122 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.7111 (mtp180) REVERT: A 1128 ARG cc_start: 0.6270 (ttp80) cc_final: 0.5764 (tpt-90) REVERT: A 1147 MET cc_start: 0.7929 (mtm) cc_final: 0.7692 (mtm) REVERT: A 1150 MET cc_start: 0.7708 (tpp) cc_final: 0.7423 (mtt) REVERT: A 1151 ASP cc_start: 0.7496 (m-30) cc_final: 0.7258 (m-30) REVERT: A 1157 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7189 (mtt) REVERT: B 55 LYS cc_start: 0.7179 (mttt) cc_final: 0.6883 (mppt) REVERT: B 60 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6214 (mt-10) REVERT: B 132 GLN cc_start: 0.7440 (tt0) cc_final: 0.7159 (tp-100) REVERT: B 139 ASP cc_start: 0.7167 (m-30) cc_final: 0.6889 (m-30) REVERT: B 166 LYS cc_start: 0.7575 (tttm) cc_final: 0.7122 (mptp) REVERT: B 371 ASP cc_start: 0.7313 (t70) cc_final: 0.6991 (m-30) REVERT: B 395 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6529 (mp0) REVERT: B 456 MET cc_start: 0.7766 (mtm) cc_final: 0.7536 (mtm) REVERT: B 464 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6442 (mt-10) REVERT: B 516 GLN cc_start: 0.6983 (tt0) cc_final: 0.6724 (tm130) REVERT: B 517 ARG cc_start: 0.6359 (mtp180) cc_final: 0.5963 (mtp85) REVERT: B 521 LEU cc_start: 0.6810 (mt) cc_final: 0.6544 (mp) REVERT: B 659 GLN cc_start: 0.7263 (mt0) cc_final: 0.6747 (mt0) REVERT: B 663 LYS cc_start: 0.8087 (tptm) cc_final: 0.7733 (mtpt) REVERT: B 667 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: B 694 MET cc_start: 0.4215 (ttp) cc_final: 0.3999 (ttm) REVERT: B 854 MET cc_start: 0.6902 (ttm) cc_final: 0.6678 (ttp) REVERT: B 916 ARG cc_start: 0.8196 (tpm170) cc_final: 0.7916 (tmm-80) REVERT: B 969 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8062 (mtm-85) REVERT: B 1042 MET cc_start: 0.8601 (mtm) cc_final: 0.8276 (mmm) REVERT: B 1046 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: B 1122 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.6629 (mtm-85) REVERT: B 1128 ARG cc_start: 0.6271 (ttp80) cc_final: 0.5763 (tpt-90) REVERT: B 1147 MET cc_start: 0.8056 (mtm) cc_final: 0.7833 (mtm) REVERT: B 1207 HIS cc_start: 0.7043 (m90) cc_final: 0.6778 (m-70) REVERT: C 55 LYS cc_start: 0.7172 (mttt) cc_final: 0.6873 (mppt) REVERT: C 60 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6199 (mt-10) REVERT: C 132 GLN cc_start: 0.7432 (tt0) cc_final: 0.7153 (tp-100) REVERT: C 139 ASP cc_start: 0.7164 (m-30) cc_final: 0.6883 (m-30) REVERT: C 166 LYS cc_start: 0.7581 (tttm) cc_final: 0.7132 (mptp) REVERT: C 371 ASP cc_start: 0.7329 (t70) cc_final: 0.7014 (m-30) REVERT: C 395 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6522 (mp0) REVERT: C 456 MET cc_start: 0.7764 (mtm) cc_final: 0.7535 (mtm) REVERT: C 464 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6449 (mt-10) REVERT: C 516 GLN cc_start: 0.6958 (tt0) cc_final: 0.6694 (tm130) REVERT: C 517 ARG cc_start: 0.6336 (mtp180) cc_final: 0.5943 (mtp85) REVERT: C 521 LEU cc_start: 0.6851 (mt) cc_final: 0.6601 (mp) REVERT: C 659 GLN cc_start: 0.7263 (mt0) cc_final: 0.6748 (mt0) REVERT: C 663 LYS cc_start: 0.8098 (tptm) cc_final: 0.7741 (mtpt) REVERT: C 667 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: C 694 MET cc_start: 0.4213 (ttp) cc_final: 0.3997 (ttm) REVERT: C 854 MET cc_start: 0.6907 (ttm) cc_final: 0.6683 (ttp) REVERT: C 916 ARG cc_start: 0.8196 (tpm170) cc_final: 0.7915 (tmm-80) REVERT: C 969 ARG cc_start: 0.8361 (mtm110) cc_final: 0.8073 (mtm-85) REVERT: C 1042 MET cc_start: 0.8614 (mtm) cc_final: 0.8286 (mmm) REVERT: C 1046 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: C 1122 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.7045 (mtp180) REVERT: C 1128 ARG cc_start: 0.6272 (ttp80) cc_final: 0.5766 (tpt-90) REVERT: C 1147 MET cc_start: 0.8151 (mtm) cc_final: 0.7668 (mtm) REVERT: C 1151 ASP cc_start: 0.7671 (m-30) cc_final: 0.7409 (m-30) REVERT: C 1207 HIS cc_start: 0.7040 (m90) cc_final: 0.6777 (m-70) REVERT: D 55 LYS cc_start: 0.7177 (mttt) cc_final: 0.6881 (mppt) REVERT: D 60 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6206 (mt-10) REVERT: D 132 GLN cc_start: 0.7420 (tt0) cc_final: 0.7151 (tp-100) REVERT: D 139 ASP cc_start: 0.7159 (m-30) cc_final: 0.6878 (m-30) REVERT: D 166 LYS cc_start: 0.7573 (tttm) cc_final: 0.7124 (mptp) REVERT: D 371 ASP cc_start: 0.7339 (t70) cc_final: 0.7021 (m-30) REVERT: D 395 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6518 (mp0) REVERT: D 456 MET cc_start: 0.7770 (mtm) cc_final: 0.7542 (mtm) REVERT: D 464 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6423 (mt-10) REVERT: D 516 GLN cc_start: 0.6963 (tt0) cc_final: 0.6699 (tm130) REVERT: D 517 ARG cc_start: 0.6350 (mtp180) cc_final: 0.5953 (mtp85) REVERT: D 521 LEU cc_start: 0.6827 (mt) cc_final: 0.6572 (mp) REVERT: D 659 GLN cc_start: 0.7271 (mt0) cc_final: 0.6759 (mt0) REVERT: D 663 LYS cc_start: 0.8085 (tptm) cc_final: 0.7730 (mtpt) REVERT: D 667 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: D 694 MET cc_start: 0.4205 (ttp) cc_final: 0.3987 (ttm) REVERT: D 854 MET cc_start: 0.6903 (ttm) cc_final: 0.6681 (ttp) REVERT: D 916 ARG cc_start: 0.8195 (tpm170) cc_final: 0.7909 (tmm-80) REVERT: D 969 ARG cc_start: 0.8362 (mtm110) cc_final: 0.8065 (mtm-85) REVERT: D 1042 MET cc_start: 0.8614 (mtm) cc_final: 0.8289 (mmm) REVERT: D 1046 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: D 1122 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.7040 (mtp180) REVERT: D 1128 ARG cc_start: 0.6271 (ttp80) cc_final: 0.5763 (tpt-90) REVERT: D 1151 ASP cc_start: 0.7543 (m-30) cc_final: 0.7289 (m-30) REVERT: D 1207 HIS cc_start: 0.7046 (m90) cc_final: 0.6783 (m-70) outliers start: 59 outliers final: 37 residues processed: 583 average time/residue: 0.5149 time to fit residues: 362.3187 Evaluate side-chains 600 residues out of total 4692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 553 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1106 LYS Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1230 LYS Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 865 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1106 LYS Chi-restraints excluded: chain B residue 1230 LYS Chi-restraints excluded: chain B residue 1405 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1106 LYS Chi-restraints excluded: chain C residue 1405 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1106 LYS Chi-restraints excluded: chain D residue 1230 LYS Chi-restraints excluded: chain D residue 1405 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 155 optimal weight: 1.9990 chunk 528 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 418 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 476 optimal weight: 0.9980 chunk 493 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN C 696 ASN D 696 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.174037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139890 restraints weight = 41983.565| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.37 r_work: 0.3323 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43736 Z= 0.134 Angle : 0.530 8.895 59468 Z= 0.276 Chirality : 0.039 0.209 6728 Planarity : 0.004 0.040 7572 Dihedral : 6.581 124.222 6820 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.48 % Allowed : 12.08 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.11), residues: 5468 helix: 2.29 (0.09), residues: 3056 sheet: -0.74 (0.22), residues: 428 loop : -0.08 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.019 0.002 TYR D 917 PHE 0.022 0.002 PHE D 879 TRP 0.016 0.002 TRP A1366 HIS 0.007 0.001 HIS C 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (43732) covalent geometry : angle 0.53044 / 0.28 (59460) SS BOND : bond 0.00013 / 0.01 ( 4) SS BOND : angle 0.29787 / 0.18 ( 8) hydrogen bonds : bond 0.04395 / 2.93 ( 2372) hydrogen bonds : angle 3.98503 / 2.90 ( 6984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25002.12 seconds wall clock time: 423 minutes 25.36 seconds (25405.36 seconds total)