Starting phenix.real_space_refine on Thu Aug 6 20:07:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wup_66267/08_2026/9wup_66267.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wup_66267/08_2026/9wup_66267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wup_66267/08_2026/9wup_66267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wup_66267/08_2026/9wup_66267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wup_66267/08_2026/9wup_66267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wup_66267/08_2026/9wup_66267.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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 Fe 2 7.16 5 P 12 5.49 5 S 68 5.16 5 C 10546 2.51 5 N 2866 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16672 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8177 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 1 Chain: "B" Number of atoms: 8177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8177 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 1 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NDP:plan-1': 1, 'NDP:plan-4': 1, 'NDP:plan-5': 1, 'NDP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NDP:plan-1': 1, 'NDP:plan-4': 1, 'NDP:plan-5': 1, 'NDP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3259 SG CYS A 404 84.321 71.338 87.208 1.00 53.31 S ATOM 11436 SG CYS B 404 34.235 90.470 43.285 1.00 36.41 S Time building chain proxies: 4.06, per 1000 atoms: 0.24 Number of scatterers: 16672 At special positions: 0 Unit cell: (111.12, 123.158, 132.418, 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) Fe 2 26.01 S 68 16.00 P 12 15.00 O 3178 8.00 N 2866 7.00 C 10546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 746.0 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 20 sheets defined 49.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.626A pdb=" N SER A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.644A pdb=" N LYS A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.627A pdb=" N ARG A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 removed outlier: 3.763A pdb=" N SER A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 173 through 192 removed outlier: 3.508A pdb=" N THR A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 227 removed outlier: 3.603A pdb=" N LYS A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.615A pdb=" N GLY A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.589A pdb=" N LYS A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.626A pdb=" N GLY A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.520A pdb=" N ARG A 402 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 removed outlier: 3.731A pdb=" N THR A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 524 Processing helix chain 'A' and resid 534 through 537 removed outlier: 4.063A pdb=" N ILE A 537 " --> pdb=" O ASN A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 537' Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'A' and resid 596 through 608 Processing helix chain 'A' and resid 625 through 645 removed outlier: 3.505A pdb=" N GLN A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.921A pdb=" N GLY A 696 " --> pdb=" O PRO A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.513A pdb=" N LEU A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.700A pdb=" N GLU A 810 " --> pdb=" O GLY A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 926 through 941 removed outlier: 3.737A pdb=" N GLY A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 992 through 1000 removed outlier: 3.826A pdb=" N VAL A 996 " --> pdb=" O TYR A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1022 through 1039 removed outlier: 3.798A pdb=" N GLU A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1056 Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.601A pdb=" N SER B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.738A pdb=" N LYS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N PHE B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.659A pdb=" N ARG B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 removed outlier: 3.847A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.699A pdb=" N LYS B 115 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 3.515A pdb=" N MET B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 173 through 191 removed outlier: 3.586A pdb=" N THR B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN B 191 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 227 removed outlier: 3.725A pdb=" N LYS B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 253 through 282 removed outlier: 4.748A pdb=" N GLU B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 273 " --> pdb=" O HIS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.867A pdb=" N ARG B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 385 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 508 through 523 Processing helix chain 'B' and resid 534 through 537 removed outlier: 3.881A pdb=" N ILE B 537 " --> pdb=" O ASN B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 537' Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 596 through 609 Processing helix chain 'B' and resid 625 through 645 Processing helix chain 'B' and resid 725 through 736 Processing helix chain 'B' and resid 764 through 771 removed outlier: 3.632A pdb=" N TYR B 770 " --> pdb=" O ASP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 792 through 802 Processing helix chain 'B' and resid 806 through 812 removed outlier: 3.547A pdb=" N GLU B 810 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 832 through 840 Processing helix chain 'B' and resid 881 through 890 Processing helix chain 'B' and resid 922 through 925 Processing helix chain 'B' and resid 926 through 942 removed outlier: 3.545A pdb=" N GLY B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 992 through 1000 removed outlier: 3.670A pdb=" N VAL B 996 " --> pdb=" O TYR B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1011 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 4.205A pdb=" N GLU B1026 " --> pdb=" O ARG B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1056 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.533A pdb=" N ARG A 356 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 334 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.558A pdb=" N GLN A 451 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 344 removed outlier: 3.535A pdb=" N THR A 342 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 532 removed outlier: 6.373A pdb=" N VAL A 546 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 584 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 548 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS A 586 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 550 " --> pdb=" O CYS A 586 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 532 removed outlier: 6.373A pdb=" N VAL A 546 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 584 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 548 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS A 586 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 550 " --> pdb=" O CYS A 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 665 removed outlier: 4.444A pdb=" N GLN B 743 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 846 through 849 removed outlier: 3.733A pdb=" N LYS A 683 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A 703 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A 687 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS A 701 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 689 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR A 699 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 761 through 763 removed outlier: 4.364A pdb=" N GLN A 743 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 869 through 871 Processing sheet with id=AB2, first strand: chain 'A' and resid 977 through 982 removed outlier: 6.805A pdb=" N ALA A 949 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 979 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 951 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA A 981 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE A 953 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 954 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 918 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N CYS A1017 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 920 " --> pdb=" O CYS A1017 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASP A1019 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1014 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP A1062 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A1016 " --> pdb=" O ASP A1062 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TRP A1064 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A1018 " --> pdb=" O TRP A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 46 removed outlier: 3.667A pdb=" N ARG B 356 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 334 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.572A pdb=" N GLN B 451 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 453 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AB7, first strand: chain 'B' and resid 528 through 532 removed outlier: 6.279A pdb=" N VAL B 546 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE B 584 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 548 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N CYS B 586 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR B 550 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 581 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 528 through 532 removed outlier: 6.279A pdb=" N VAL B 546 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE B 584 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 548 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N CYS B 586 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR B 550 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N GLY B 618 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 583 " --> pdb=" O GLY B 618 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLY B 620 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY B 585 " --> pdb=" O GLY B 620 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 846 through 849 removed outlier: 4.565A pdb=" N MET B 897 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 683 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B 703 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B 687 " --> pdb=" O HIS B 701 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS B 701 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLU B 689 " --> pdb=" O THR B 699 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR B 699 " --> pdb=" O GLU B 689 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 869 through 871 Processing sheet with id=AC2, first strand: chain 'B' and resid 977 through 982 removed outlier: 7.063A pdb=" N ALA B 949 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR B 979 " --> pdb=" O ALA B 949 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 951 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA B 981 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE B 953 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 918 " --> pdb=" O TYR B1015 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N CYS B1017 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 920 " --> pdb=" O CYS B1017 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASP B1019 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B1014 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP B1062 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B1016 " --> pdb=" O ASP B1062 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TRP B1064 " --> pdb=" O ILE B1016 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY B1018 " --> pdb=" O TRP B1064 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2256 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: 3.65 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6896 1.39 - 1.57: 10014 1.57 - 1.75: 18 1.75 - 1.93: 123 1.93 - 2.11: 7 Bond restraints: 17058 Sorted by residual: bond pdb=" C4 FMN B1103 " pdb=" C4A FMN B1103 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C4 FMN A1102 " pdb=" C4A FMN A1102 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C4A FMN A1102 " pdb=" N5 FMN A1102 " ideal model delta sigma weight residual 1.300 1.379 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C4A FMN B1103 " pdb=" N5 FMN B1103 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C3B HEM A1101 " pdb=" CAB HEM A1101 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 17053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 22542 1.36 - 2.72: 430 2.72 - 4.08: 117 4.08 - 5.44: 40 5.44 - 6.80: 17 Bond angle restraints: 23146 Sorted by residual: angle pdb=" C VAL A 375 " pdb=" N GLU A 376 " pdb=" CA GLU A 376 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C ASP A 374 " pdb=" N VAL A 375 " pdb=" CA VAL A 375 " ideal model delta sigma weight residual 121.97 127.83 -5.86 1.80e+00 3.09e-01 1.06e+01 angle pdb=" N VAL A 375 " pdb=" CA VAL A 375 " pdb=" C VAL A 375 " ideal model delta sigma weight residual 109.34 115.69 -6.35 2.08e+00 2.31e-01 9.33e+00 angle pdb=" C SER B 304 " pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.43e+00 angle pdb=" CA ARG A 936 " pdb=" CB ARG A 936 " pdb=" CG ARG A 936 " ideal model delta sigma weight residual 114.10 119.46 -5.36 2.00e+00 2.50e-01 7.17e+00 ... (remaining 23141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 8998 22.63 - 45.26: 1043 45.26 - 67.89: 182 67.89 - 90.52: 43 90.52 - 113.15: 2 Dihedral angle restraints: 10268 sinusoidal: 4336 harmonic: 5932 Sorted by residual: dihedral pdb=" C5B NDP B1104 " pdb=" O5B NDP B1104 " pdb=" PA NDP B1104 " pdb=" O3 NDP B1104 " ideal model delta sinusoidal sigma weight residual 175.04 61.89 113.15 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" C5B NDP A1104 " pdb=" O5B NDP A1104 " pdb=" PA NDP A1104 " pdb=" O3 NDP A1104 " ideal model delta sinusoidal sigma weight residual 175.04 62.92 112.12 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1A HEM B1101 " pdb=" C2A HEM B1101 " pdb=" CAA HEM B1101 " pdb=" CBA HEM B1101 " ideal model delta sinusoidal sigma weight residual -180.00 -100.91 -79.09 2 2.00e+01 2.50e-03 1.16e+01 ... (remaining 10265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1492 0.027 - 0.055: 626 0.055 - 0.082: 198 0.082 - 0.109: 129 0.109 - 0.137: 27 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CA ILE A 52 " pdb=" N ILE A 52 " pdb=" C ILE A 52 " pdb=" CB ILE A 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE A 918 " pdb=" N ILE A 918 " pdb=" C ILE A 918 " pdb=" CB ILE A 918 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 7 " pdb=" N ILE A 7 " pdb=" C ILE A 7 " pdb=" CB ILE A 7 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2469 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 921 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 922 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 922 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 922 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 46 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO A 47 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 47 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 47 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 389 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 390 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 390 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 390 " -0.029 5.00e-02 4.00e+02 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 8196 2.99 - 3.47: 16840 3.47 - 3.95: 28610 3.95 - 4.42: 33725 4.42 - 4.90: 53657 Nonbonded interactions: 141028 Sorted by model distance: nonbonded pdb=" C3B NDP A1104 " pdb=" O5B NDP A1104 " model vdw 2.515 2.608 nonbonded pdb=" O THR A 659 " pdb=" OG1 THR A 659 " model vdw 2.554 3.040 nonbonded pdb=" O THR B 440 " pdb=" OG1 THR B 440 " model vdw 2.555 3.040 nonbonded pdb=" C2B NDP A1104 " pdb=" O1X NDP A1104 " model vdw 2.557 2.608 nonbonded pdb=" N ASP A 253 " pdb=" OD1 ASP A 253 " model vdw 2.589 3.120 ... (remaining 141023 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 1101 or resid 1104)) selection = (chain 'B' and (resid 5 through 1101 or resid 1104)) } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.220 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 17060 Z= 0.168 Angle : 0.539 6.797 23146 Z= 0.259 Chirality : 0.039 0.137 2472 Planarity : 0.004 0.061 2984 Dihedral : 18.839 113.155 6460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.11 % Favored : 97.79 % Rotamer: Outliers : 0.45 % Allowed : 31.44 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.19), residues: 2040 helix: 1.49 (0.18), residues: 904 sheet: 0.10 (0.30), residues: 298 loop : -0.33 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 99 TYR 0.014 0.001 TYR A 38 PHE 0.016 0.001 PHE B 69 TRP 0.014 0.001 TRP A 98 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (17058) covalent geometry : angle 0.53867 / 0.26 (23146) hydrogen bonds : bond 0.14946 / 9.75 ( 767) hydrogen bonds : angle 6.31511 / 4.47 ( 2256) Misc. bond : bond 0.08169 / 4.30 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.610 Fit side-chains REVERT: A 33 LYS cc_start: 0.7129 (mtpm) cc_final: 0.6828 (mtpt) REVERT: A 115 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7297 (mttm) REVERT: A 184 ASP cc_start: 0.8390 (t70) cc_final: 0.7959 (t0) REVERT: A 191 GLN cc_start: 0.8356 (mt0) cc_final: 0.7487 (mm-40) REVERT: A 196 GLN cc_start: 0.7627 (mp10) cc_final: 0.7050 (mt0) REVERT: A 204 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7643 (ttmm) REVERT: A 226 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7735 (ttt180) REVERT: A 291 LYS cc_start: 0.7398 (mmtt) cc_final: 0.6891 (mtpm) REVERT: A 299 GLN cc_start: 0.7573 (tt0) cc_final: 0.7368 (tm-30) REVERT: A 451 GLN cc_start: 0.8101 (tt0) cc_final: 0.7840 (tt0) REVERT: A 453 GLN cc_start: 0.7519 (mt0) cc_final: 0.7130 (tt0) REVERT: A 516 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6693 (tt0) REVERT: A 529 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7701 (mp0) REVERT: A 636 LYS cc_start: 0.7419 (mttt) cc_final: 0.7093 (mmtt) REVERT: A 726 LYS cc_start: 0.7493 (mmmt) cc_final: 0.6999 (ptmm) REVERT: A 797 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.7409 (mtm110) REVERT: A 859 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7064 (pp20) REVERT: A 972 LYS cc_start: 0.7796 (tppt) cc_final: 0.7153 (ttpp) REVERT: A 1055 LYS cc_start: 0.8039 (mttt) cc_final: 0.7736 (mmpt) REVERT: B 33 LYS cc_start: 0.7871 (tptt) cc_final: 0.7555 (ttpt) REVERT: B 162 TYR cc_start: 0.8793 (t80) cc_final: 0.8542 (t80) REVERT: B 170 GLU cc_start: 0.7559 (pm20) cc_final: 0.7299 (tm-30) REVERT: B 191 GLN cc_start: 0.8102 (pt0) cc_final: 0.7120 (mm-40) REVERT: B 233 GLU cc_start: 0.6860 (tt0) cc_final: 0.5988 (mp0) REVERT: B 291 LYS cc_start: 0.7038 (mttt) cc_final: 0.6366 (ttpp) REVERT: B 384 GLU cc_start: 0.7174 (tp30) cc_final: 0.6167 (mt-10) REVERT: B 434 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6003 (mp10) REVERT: B 438 LYS cc_start: 0.8194 (tttp) cc_final: 0.7477 (ttmt) REVERT: B 529 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 539 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6954 (mm-30) REVERT: B 635 GLU cc_start: 0.7242 (pp20) cc_final: 0.6853 (pt0) REVERT: B 726 LYS cc_start: 0.8029 (mttm) cc_final: 0.7313 (tptt) REVERT: B 739 ASN cc_start: 0.8103 (t0) cc_final: 0.7619 (t0) REVERT: B 814 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8162 (tppp) REVERT: B 815 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8484 (mttm) REVERT: B 912 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6971 (mp0) REVERT: B 937 ASP cc_start: 0.7532 (t70) cc_final: 0.6933 (t0) REVERT: B 1000 ASN cc_start: 0.7777 (m-40) cc_final: 0.7462 (m110) REVERT: B 1022 ARG cc_start: 0.6647 (ttp80) cc_final: 0.6160 (ttp80) REVERT: B 1044 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6378 (mp10) outliers start: 8 outliers final: 2 residues processed: 232 average time/residue: 0.6972 time to fit residues: 177.9193 Evaluate side-chains 218 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 920 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 130 GLN B 242 ASN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.162706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134137 restraints weight = 19345.258| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.69 r_work: 0.3412 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17060 Z= 0.111 Angle : 0.494 6.415 23146 Z= 0.251 Chirality : 0.039 0.145 2472 Planarity : 0.004 0.053 2984 Dihedral : 7.616 111.417 2378 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 3.75 % Allowed : 26.33 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.19), residues: 2040 helix: 1.58 (0.17), residues: 904 sheet: 0.02 (0.29), residues: 310 loop : -0.29 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.009 0.001 TYR A 503 PHE 0.016 0.001 PHE B 160 TRP 0.013 0.001 TRP A 98 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (17058) covalent geometry : angle 0.49396 / 0.25 (23146) hydrogen bonds : bond 0.04033 / 2.63 ( 767) hydrogen bonds : angle 4.70914 / 3.34 ( 2256) Misc. bond : bond 0.01373 / 0.72 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 0.612 Fit side-chains REVERT: A 33 LYS cc_start: 0.7378 (mtpm) cc_final: 0.7096 (mtpt) REVERT: A 115 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7370 (mttm) REVERT: A 134 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6428 (mtm-85) REVERT: A 184 ASP cc_start: 0.8274 (t70) cc_final: 0.7858 (t0) REVERT: A 191 GLN cc_start: 0.8253 (mt0) cc_final: 0.7430 (mm-40) REVERT: A 204 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7642 (ttmm) REVERT: A 226 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7770 (ttt180) REVERT: A 291 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7069 (mtpm) REVERT: A 451 GLN cc_start: 0.7837 (tt0) cc_final: 0.7588 (tt0) REVERT: A 453 GLN cc_start: 0.7305 (mt0) cc_final: 0.6965 (tt0) REVERT: A 516 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6789 (tt0) REVERT: A 529 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7608 (mp0) REVERT: A 634 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7803 (mtpt) REVERT: A 636 LYS cc_start: 0.7298 (mttt) cc_final: 0.7084 (tmtt) REVERT: A 726 LYS cc_start: 0.7540 (mmmt) cc_final: 0.7006 (ptmm) REVERT: A 797 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7450 (mtm110) REVERT: A 831 MET cc_start: 0.8258 (ttp) cc_final: 0.7829 (ttm) REVERT: A 859 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7087 (pp20) REVERT: A 895 ASP cc_start: 0.8234 (m-30) cc_final: 0.8026 (m-30) REVERT: A 972 LYS cc_start: 0.8014 (tppt) cc_final: 0.7432 (ttpp) REVERT: A 976 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7386 (pmt) REVERT: A 1055 LYS cc_start: 0.8096 (mttt) cc_final: 0.7801 (mmpt) REVERT: B 6 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7038 (pp) REVERT: B 33 LYS cc_start: 0.7597 (tptt) cc_final: 0.7262 (ttpt) REVERT: B 120 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6576 (mtm) REVERT: B 162 TYR cc_start: 0.8787 (t80) cc_final: 0.8506 (t80) REVERT: B 170 GLU cc_start: 0.7547 (pm20) cc_final: 0.7280 (tm-30) REVERT: B 191 GLN cc_start: 0.8164 (pt0) cc_final: 0.7089 (mm-40) REVERT: B 217 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7641 (tm) REVERT: B 233 GLU cc_start: 0.6850 (tt0) cc_final: 0.5916 (mp0) REVERT: B 312 LEU cc_start: 0.7610 (mp) cc_final: 0.7380 (mp) REVERT: B 434 GLN cc_start: 0.6868 (mm-40) cc_final: 0.5940 (mp10) REVERT: B 438 LYS cc_start: 0.8029 (tttp) cc_final: 0.7268 (ttmt) REVERT: B 527 HIS cc_start: 0.7380 (t-90) cc_final: 0.6894 (t-90) REVERT: B 529 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: B 539 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6798 (mm-30) REVERT: B 635 GLU cc_start: 0.7208 (pp20) cc_final: 0.6783 (pt0) REVERT: B 697 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6572 (ptm-80) REVERT: B 726 LYS cc_start: 0.7848 (mttm) cc_final: 0.7247 (mptp) REVERT: B 739 ASN cc_start: 0.7935 (t0) cc_final: 0.7496 (t0) REVERT: B 776 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: B 814 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8036 (tppp) REVERT: B 815 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8294 (mttm) REVERT: B 937 ASP cc_start: 0.7465 (t70) cc_final: 0.6873 (t0) REVERT: B 1022 ARG cc_start: 0.6657 (ttp80) cc_final: 0.6171 (ttp80) REVERT: B 1044 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6274 (mp10) outliers start: 66 outliers final: 26 residues processed: 270 average time/residue: 0.6693 time to fit residues: 199.2579 Evaluate side-chains 247 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN B 130 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN B 885 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124456 restraints weight = 19772.759| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.66 r_work: 0.3315 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 17060 Z= 0.318 Angle : 0.691 7.483 23146 Z= 0.348 Chirality : 0.048 0.241 2472 Planarity : 0.006 0.055 2984 Dihedral : 8.167 118.115 2378 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 5.16 % Allowed : 24.18 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2040 helix: 0.90 (0.17), residues: 896 sheet: -0.44 (0.27), residues: 314 loop : -0.48 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 600 TYR 0.025 0.002 TYR A 848 PHE 0.024 0.003 PHE B 160 TRP 0.021 0.002 TRP A 98 HIS 0.012 0.002 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.32 (17058) covalent geometry : angle 0.69098 / 0.35 (23146) hydrogen bonds : bond 0.05502 / 3.61 ( 767) hydrogen bonds : angle 4.84487 / 3.43 ( 2256) Misc. bond : bond 0.03401 / 1.77 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 230 time to evaluate : 0.831 Fit side-chains REVERT: A 33 LYS cc_start: 0.7555 (mtpm) cc_final: 0.7088 (mtpt) REVERT: A 58 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: A 59 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7069 (mp) REVERT: A 112 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6722 (tpp80) REVERT: A 115 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7408 (mttm) REVERT: A 134 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6639 (mtm-85) REVERT: A 184 ASP cc_start: 0.8439 (t70) cc_final: 0.8066 (t0) REVERT: A 196 GLN cc_start: 0.7542 (mp10) cc_final: 0.6921 (mt0) REVERT: A 291 LYS cc_start: 0.7496 (mmtt) cc_final: 0.6829 (mtpm) REVERT: A 295 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7375 (mm-30) REVERT: A 451 GLN cc_start: 0.8101 (tt0) cc_final: 0.7764 (tt0) REVERT: A 453 GLN cc_start: 0.7314 (mt0) cc_final: 0.6954 (tt0) REVERT: A 516 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6904 (tt0) REVERT: A 529 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 634 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7875 (mtpt) REVERT: A 726 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7133 (ptmm) REVERT: A 797 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7503 (mtm110) REVERT: A 941 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7013 (mt0) REVERT: A 958 GLU cc_start: 0.7012 (mp0) cc_final: 0.6215 (pp20) REVERT: A 972 LYS cc_start: 0.7877 (tppt) cc_final: 0.7359 (ttpp) REVERT: A 976 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7338 (pmt) REVERT: A 997 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6829 (mtt) REVERT: A 1055 LYS cc_start: 0.8213 (mttt) cc_final: 0.7964 (mmtt) REVERT: B 6 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7071 (pp) REVERT: B 33 LYS cc_start: 0.7623 (tptt) cc_final: 0.7286 (ttpt) REVERT: B 120 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: B 170 GLU cc_start: 0.7816 (pm20) cc_final: 0.7518 (tm-30) REVERT: B 195 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6491 (pt) REVERT: B 217 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7969 (tm) REVERT: B 434 GLN cc_start: 0.6952 (mm-40) cc_final: 0.6075 (mp10) REVERT: B 438 LYS cc_start: 0.8193 (tttp) cc_final: 0.7446 (ttmt) REVERT: B 529 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: B 539 GLU cc_start: 0.7755 (mt-10) cc_final: 0.6986 (mm-30) REVERT: B 635 GLU cc_start: 0.7234 (pp20) cc_final: 0.6803 (pt0) REVERT: B 697 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6778 (ptm-80) REVERT: B 726 LYS cc_start: 0.8101 (mttm) cc_final: 0.7472 (mmmt) REVERT: B 739 ASN cc_start: 0.8044 (t0) cc_final: 0.7441 (t0) REVERT: B 776 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: B 811 GLN cc_start: 0.8403 (mt0) cc_final: 0.8185 (mt0) REVERT: B 814 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8030 (tppp) REVERT: B 815 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8313 (mttm) REVERT: B 891 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8035 (mmtm) REVERT: B 1022 ARG cc_start: 0.6766 (ttp80) cc_final: 0.6211 (ttp80) outliers start: 91 outliers final: 39 residues processed: 297 average time/residue: 0.6686 time to fit residues: 219.0788 Evaluate side-chains 270 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1031 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 130 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS A1000 ASN B 286 ASN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129432 restraints weight = 19438.994| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.67 r_work: 0.3377 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17060 Z= 0.119 Angle : 0.506 7.233 23146 Z= 0.258 Chirality : 0.040 0.139 2472 Planarity : 0.004 0.055 2984 Dihedral : 7.845 117.400 2378 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 4.48 % Allowed : 25.43 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2040 helix: 1.23 (0.17), residues: 906 sheet: -0.30 (0.27), residues: 308 loop : -0.41 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.015 0.001 TYR A 281 PHE 0.016 0.001 PHE B 160 TRP 0.016 0.001 TRP A 98 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (17058) covalent geometry : angle 0.50587 / 0.26 (23146) hydrogen bonds : bond 0.03901 / 2.54 ( 767) hydrogen bonds : angle 4.40751 / 3.13 ( 2256) Misc. bond : bond 0.01091 / 0.57 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 226 time to evaluate : 0.477 Fit side-chains REVERT: A 33 LYS cc_start: 0.7476 (mtpm) cc_final: 0.7125 (mtpt) REVERT: A 59 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6810 (mp) REVERT: A 115 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7372 (mttm) REVERT: A 134 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6580 (mtm-85) REVERT: A 184 ASP cc_start: 0.8274 (t70) cc_final: 0.7921 (t0) REVERT: A 191 GLN cc_start: 0.8298 (mt0) cc_final: 0.7565 (mm-40) REVERT: A 291 LYS cc_start: 0.7437 (mmtt) cc_final: 0.6981 (mtpm) REVERT: A 451 GLN cc_start: 0.7983 (tt0) cc_final: 0.7704 (tt0) REVERT: A 453 GLN cc_start: 0.7310 (mt0) cc_final: 0.6914 (tt0) REVERT: A 516 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6829 (tt0) REVERT: A 529 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7606 (mp0) REVERT: A 726 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7106 (ptmm) REVERT: A 797 ARG cc_start: 0.7720 (ttp-110) cc_final: 0.7447 (mtm110) REVERT: A 859 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7239 (pp20) REVERT: A 941 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6886 (mt0) REVERT: A 956 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7035 (mtt90) REVERT: A 958 GLU cc_start: 0.6906 (mp0) cc_final: 0.6105 (pp20) REVERT: A 968 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 972 LYS cc_start: 0.7938 (tppt) cc_final: 0.7379 (ttpp) REVERT: A 976 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7293 (pmt) REVERT: A 997 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6388 (mmt) REVERT: A 1055 LYS cc_start: 0.8187 (mttt) cc_final: 0.7847 (mmtt) REVERT: B 33 LYS cc_start: 0.7576 (tptt) cc_final: 0.7274 (ttpt) REVERT: B 120 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6953 (mtm) REVERT: B 162 TYR cc_start: 0.8908 (t80) cc_final: 0.8649 (t80) REVERT: B 170 GLU cc_start: 0.7809 (pm20) cc_final: 0.7466 (tm-30) REVERT: B 191 GLN cc_start: 0.8190 (pt0) cc_final: 0.7166 (mm-40) REVERT: B 195 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6404 (pt) REVERT: B 217 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7827 (tm) REVERT: B 351 LYS cc_start: 0.7584 (tppt) cc_final: 0.6816 (mtpt) REVERT: B 434 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6041 (mp10) REVERT: B 438 LYS cc_start: 0.8096 (tttp) cc_final: 0.7370 (ttmt) REVERT: B 529 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: B 539 GLU cc_start: 0.7701 (mt-10) cc_final: 0.6926 (mm-30) REVERT: B 543 GLU cc_start: 0.7431 (pt0) cc_final: 0.7171 (pm20) REVERT: B 635 GLU cc_start: 0.7082 (pp20) cc_final: 0.6706 (pt0) REVERT: B 697 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6659 (ptm-80) REVERT: B 726 LYS cc_start: 0.8027 (mttm) cc_final: 0.7407 (mptp) REVERT: B 739 ASN cc_start: 0.8013 (t0) cc_final: 0.7366 (t0) REVERT: B 811 GLN cc_start: 0.8393 (mt0) cc_final: 0.8176 (mt0) REVERT: B 814 LYS cc_start: 0.8381 (ttpp) cc_final: 0.7980 (tppp) REVERT: B 815 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8300 (mttm) REVERT: B 891 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7933 (mmtm) REVERT: B 1022 ARG cc_start: 0.6753 (ttp80) cc_final: 0.6192 (ttp80) outliers start: 79 outliers final: 30 residues processed: 286 average time/residue: 0.6472 time to fit residues: 203.6396 Evaluate side-chains 259 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1031 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS B 130 GLN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129808 restraints weight = 19474.300| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.70 r_work: 0.3356 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17060 Z= 0.122 Angle : 0.505 6.958 23146 Z= 0.256 Chirality : 0.040 0.133 2472 Planarity : 0.004 0.048 2984 Dihedral : 7.724 117.434 2378 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 4.03 % Allowed : 25.71 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.19), residues: 2040 helix: 1.36 (0.17), residues: 908 sheet: -0.29 (0.28), residues: 310 loop : -0.35 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.017 0.001 TYR A 281 PHE 0.017 0.001 PHE B 69 TRP 0.015 0.001 TRP A 98 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (17058) covalent geometry : angle 0.50522 / 0.26 (23146) hydrogen bonds : bond 0.03735 / 2.44 ( 767) hydrogen bonds : angle 4.26273 / 3.02 ( 2256) Misc. bond : bond 0.01116 / 0.59 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.546 Fit side-chains REVERT: A 33 LYS cc_start: 0.7468 (mtpm) cc_final: 0.7129 (mtpt) REVERT: A 58 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: A 112 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7149 (tmt90) REVERT: A 115 LYS cc_start: 0.7636 (mtpp) cc_final: 0.7364 (mttm) REVERT: A 134 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6573 (mtm-85) REVERT: A 184 ASP cc_start: 0.8323 (t70) cc_final: 0.7915 (t0) REVERT: A 191 GLN cc_start: 0.8321 (mt0) cc_final: 0.7601 (mm-40) REVERT: A 291 LYS cc_start: 0.7410 (mmtt) cc_final: 0.6956 (mtpm) REVERT: A 451 GLN cc_start: 0.7863 (tt0) cc_final: 0.7587 (tt0) REVERT: A 453 GLN cc_start: 0.7350 (mt0) cc_final: 0.6901 (tt0) REVERT: A 516 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6818 (tt0) REVERT: A 529 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7646 (mp0) REVERT: A 726 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7101 (ptmm) REVERT: A 797 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7401 (mtm110) REVERT: A 859 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7317 (pp20) REVERT: A 956 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7038 (mtt90) REVERT: A 958 GLU cc_start: 0.6873 (mp0) cc_final: 0.6125 (pp20) REVERT: A 972 LYS cc_start: 0.7955 (tppt) cc_final: 0.7362 (ttpp) REVERT: A 976 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7287 (pmt) REVERT: A 1055 LYS cc_start: 0.8214 (mttt) cc_final: 0.7861 (mmtt) REVERT: B 6 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7037 (pp) REVERT: B 33 LYS cc_start: 0.7627 (tptt) cc_final: 0.7272 (ttpt) REVERT: B 120 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6999 (mtm) REVERT: B 162 TYR cc_start: 0.8912 (t80) cc_final: 0.8632 (t80) REVERT: B 170 GLU cc_start: 0.7854 (pm20) cc_final: 0.7490 (tm-30) REVERT: B 191 GLN cc_start: 0.8215 (pt0) cc_final: 0.7192 (mm-40) REVERT: B 195 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6507 (pt) REVERT: B 217 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7812 (tm) REVERT: B 233 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5904 (pm20) REVERT: B 351 LYS cc_start: 0.7580 (tppt) cc_final: 0.6809 (mtpt) REVERT: B 434 GLN cc_start: 0.6779 (mm-40) cc_final: 0.5993 (mp10) REVERT: B 438 LYS cc_start: 0.8099 (tttp) cc_final: 0.7352 (ttmt) REVERT: B 529 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: B 539 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7000 (mm-30) REVERT: B 543 GLU cc_start: 0.7481 (pt0) cc_final: 0.7222 (pm20) REVERT: B 608 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: B 635 GLU cc_start: 0.7259 (pp20) cc_final: 0.6854 (pt0) REVERT: B 697 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6677 (ptm-80) REVERT: B 726 LYS cc_start: 0.7980 (mttm) cc_final: 0.7383 (mptp) REVERT: B 739 ASN cc_start: 0.8064 (t0) cc_final: 0.7432 (t0) REVERT: B 810 GLU cc_start: 0.7950 (tt0) cc_final: 0.7551 (tm-30) REVERT: B 814 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7992 (tppp) REVERT: B 815 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8291 (mttm) REVERT: B 891 LYS cc_start: 0.8315 (mmtm) cc_final: 0.7834 (mmtm) REVERT: B 1022 ARG cc_start: 0.6691 (ttp80) cc_final: 0.6126 (ttp80) REVERT: B 1044 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6275 (mp10) outliers start: 71 outliers final: 34 residues processed: 285 average time/residue: 0.7247 time to fit residues: 226.6570 Evaluate side-chains 268 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 920 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 527 HIS B 130 GLN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128119 restraints weight = 19396.265| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.65 r_work: 0.3342 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17060 Z= 0.157 Angle : 0.538 6.661 23146 Z= 0.272 Chirality : 0.041 0.141 2472 Planarity : 0.004 0.048 2984 Dihedral : 7.792 117.345 2378 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 4.54 % Allowed : 25.14 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.18), residues: 2040 helix: 1.26 (0.17), residues: 910 sheet: -0.42 (0.28), residues: 294 loop : -0.32 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.017 0.001 TYR A 281 PHE 0.017 0.002 PHE B 160 TRP 0.017 0.001 TRP A 98 HIS 0.009 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (17058) covalent geometry : angle 0.53771 / 0.27 (23146) hydrogen bonds : bond 0.04053 / 2.65 ( 767) hydrogen bonds : angle 4.31555 / 3.05 ( 2256) Misc. bond : bond 0.01570 / 0.82 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 223 time to evaluate : 0.457 Fit side-chains REVERT: A 33 LYS cc_start: 0.7487 (mtpm) cc_final: 0.7148 (mtpt) REVERT: A 58 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: A 112 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6675 (tpp80) REVERT: A 115 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7369 (mttm) REVERT: A 134 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6597 (mtm-85) REVERT: A 184 ASP cc_start: 0.8319 (t70) cc_final: 0.7961 (t0) REVERT: A 191 GLN cc_start: 0.8282 (mt0) cc_final: 0.7571 (mm-40) REVERT: A 453 GLN cc_start: 0.7319 (mt0) cc_final: 0.6871 (tt0) REVERT: A 516 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6868 (tt0) REVERT: A 529 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7610 (mp0) REVERT: A 726 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7094 (ptmm) REVERT: A 797 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7411 (mtm110) REVERT: A 859 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7308 (pp20) REVERT: A 941 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: A 956 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7038 (mtt90) REVERT: A 958 GLU cc_start: 0.6884 (mp0) cc_final: 0.6124 (pp20) REVERT: A 972 LYS cc_start: 0.7917 (tppt) cc_final: 0.7346 (ttpp) REVERT: A 976 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7339 (pmt) REVERT: A 1055 LYS cc_start: 0.8206 (mttt) cc_final: 0.7858 (mmtt) REVERT: B 33 LYS cc_start: 0.7623 (tptt) cc_final: 0.7297 (ttpt) REVERT: B 120 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7016 (mtm) REVERT: B 162 TYR cc_start: 0.8944 (t80) cc_final: 0.8660 (t80) REVERT: B 170 GLU cc_start: 0.7820 (pm20) cc_final: 0.7536 (tm-30) REVERT: B 191 GLN cc_start: 0.8216 (pt0) cc_final: 0.7195 (mm-40) REVERT: B 195 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6501 (pt) REVERT: B 217 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7836 (tm) REVERT: B 351 LYS cc_start: 0.7585 (tppt) cc_final: 0.6827 (mtpt) REVERT: B 434 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6039 (mp10) REVERT: B 438 LYS cc_start: 0.8119 (tttp) cc_final: 0.7372 (ttmt) REVERT: B 529 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: B 539 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7065 (mm-30) REVERT: B 543 GLU cc_start: 0.7541 (pt0) cc_final: 0.7275 (pm20) REVERT: B 608 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: B 635 GLU cc_start: 0.7290 (pp20) cc_final: 0.6901 (pt0) REVERT: B 697 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6689 (ptm-80) REVERT: B 726 LYS cc_start: 0.8023 (mttm) cc_final: 0.7412 (mptp) REVERT: B 739 ASN cc_start: 0.7965 (t0) cc_final: 0.6916 (m-40) REVERT: B 776 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: B 814 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7967 (tppp) REVERT: B 815 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8297 (mttm) REVERT: B 891 LYS cc_start: 0.8355 (mmtm) cc_final: 0.7877 (mmtm) REVERT: B 956 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7731 (mtp180) REVERT: B 1022 ARG cc_start: 0.6682 (ttp80) cc_final: 0.6140 (ttp80) outliers start: 80 outliers final: 47 residues processed: 284 average time/residue: 0.6308 time to fit residues: 196.8804 Evaluate side-chains 276 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 168 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 260 GLN A 392 HIS A 527 HIS A 994 GLN A1058 GLN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129898 restraints weight = 19314.126| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.65 r_work: 0.3363 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17060 Z= 0.118 Angle : 0.503 6.547 23146 Z= 0.255 Chirality : 0.040 0.131 2472 Planarity : 0.004 0.046 2984 Dihedral : 7.690 116.616 2378 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 4.26 % Allowed : 25.43 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.19), residues: 2040 helix: 1.40 (0.17), residues: 910 sheet: -0.37 (0.29), residues: 292 loop : -0.28 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.018 0.001 TYR A 281 PHE 0.018 0.001 PHE B 69 TRP 0.015 0.001 TRP A 98 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (17058) covalent geometry : angle 0.50266 / 0.26 (23146) hydrogen bonds : bond 0.03626 / 2.37 ( 767) hydrogen bonds : angle 4.19006 / 2.96 ( 2256) Misc. bond : bond 0.01072 / 0.56 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 0.624 Fit side-chains REVERT: A 33 LYS cc_start: 0.7473 (mtpm) cc_final: 0.7130 (mtpt) REVERT: A 58 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7183 (mm-30) REVERT: A 112 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6653 (tpp80) REVERT: A 115 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7351 (mttm) REVERT: A 134 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6665 (mtm-85) REVERT: A 184 ASP cc_start: 0.8288 (t70) cc_final: 0.7893 (t0) REVERT: A 191 GLN cc_start: 0.8300 (mt0) cc_final: 0.7606 (mm-40) REVERT: A 291 LYS cc_start: 0.7410 (mmtt) cc_final: 0.6951 (mtpm) REVERT: A 453 GLN cc_start: 0.7260 (mt0) cc_final: 0.6886 (tt0) REVERT: A 516 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6814 (tt0) REVERT: A 529 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7617 (mp0) REVERT: A 660 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 726 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7086 (ptmm) REVERT: A 734 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: A 797 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7404 (mtm110) REVERT: A 859 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7367 (pp20) REVERT: A 941 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6857 (mt0) REVERT: A 956 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6972 (mtt90) REVERT: A 958 GLU cc_start: 0.6888 (mp0) cc_final: 0.6189 (pp20) REVERT: A 968 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 972 LYS cc_start: 0.7891 (tppt) cc_final: 0.7291 (ttpp) REVERT: A 976 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7277 (pmt) REVERT: A 1055 LYS cc_start: 0.8210 (mttt) cc_final: 0.7861 (mmtt) REVERT: B 33 LYS cc_start: 0.7638 (tptt) cc_final: 0.7247 (ttpt) REVERT: B 120 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6939 (mtm) REVERT: B 162 TYR cc_start: 0.8907 (t80) cc_final: 0.8624 (t80) REVERT: B 170 GLU cc_start: 0.7835 (pm20) cc_final: 0.7494 (tm-30) REVERT: B 191 GLN cc_start: 0.8207 (pt0) cc_final: 0.7164 (mm-40) REVERT: B 195 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6503 (pt) REVERT: B 217 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7755 (tm) REVERT: B 233 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5860 (pm20) REVERT: B 351 LYS cc_start: 0.7580 (tppt) cc_final: 0.6827 (mtpt) REVERT: B 434 GLN cc_start: 0.6785 (mm-40) cc_final: 0.6004 (mp10) REVERT: B 438 LYS cc_start: 0.8080 (tttp) cc_final: 0.7340 (ttmt) REVERT: B 529 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: B 539 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7037 (mm-30) REVERT: B 543 GLU cc_start: 0.7512 (pt0) cc_final: 0.7257 (pm20) REVERT: B 608 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: B 635 GLU cc_start: 0.7258 (pp20) cc_final: 0.6872 (pt0) REVERT: B 697 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6649 (ptm-80) REVERT: B 726 LYS cc_start: 0.7990 (mttm) cc_final: 0.7398 (mptp) REVERT: B 739 ASN cc_start: 0.7929 (t0) cc_final: 0.6895 (m-40) REVERT: B 776 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: B 814 LYS cc_start: 0.8383 (ttpp) cc_final: 0.7971 (tppp) REVERT: B 815 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8291 (mttm) REVERT: B 891 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7837 (mmtm) REVERT: B 956 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7695 (mtp180) REVERT: B 1022 ARG cc_start: 0.6687 (ttp80) cc_final: 0.6147 (ttp80) outliers start: 75 outliers final: 42 residues processed: 284 average time/residue: 0.6719 time to fit residues: 209.7016 Evaluate side-chains 275 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 734 GLN Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 956 ARG Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 83 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 101 optimal weight: 0.0870 chunk 22 optimal weight: 0.0980 chunk 146 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 392 HIS A 527 HIS B 130 GLN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127103 restraints weight = 19405.853| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.65 r_work: 0.3343 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17060 Z= 0.172 Angle : 0.555 6.586 23146 Z= 0.280 Chirality : 0.042 0.146 2472 Planarity : 0.004 0.045 2984 Dihedral : 7.838 118.461 2378 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 4.48 % Allowed : 25.48 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.19), residues: 2040 helix: 1.25 (0.17), residues: 908 sheet: -0.42 (0.29), residues: 294 loop : -0.35 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 423 TYR 0.019 0.002 TYR A 281 PHE 0.018 0.002 PHE B 160 TRP 0.017 0.001 TRP A 98 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (17058) covalent geometry : angle 0.55464 / 0.28 (23146) hydrogen bonds : bond 0.04157 / 2.73 ( 767) hydrogen bonds : angle 4.32623 / 3.05 ( 2256) Misc. bond : bond 0.01680 / 0.88 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 218 time to evaluate : 0.545 Fit side-chains REVERT: A 33 LYS cc_start: 0.7489 (mtpm) cc_final: 0.7137 (mtpt) REVERT: A 58 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: A 112 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6649 (tpp80) REVERT: A 115 LYS cc_start: 0.7636 (mtpp) cc_final: 0.7344 (mttm) REVERT: A 134 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6713 (mtm-85) REVERT: A 184 ASP cc_start: 0.8294 (t70) cc_final: 0.7931 (t0) REVERT: A 191 GLN cc_start: 0.8292 (mt0) cc_final: 0.7579 (mm-40) REVERT: A 291 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6932 (mtpm) REVERT: A 379 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7198 (ttm170) REVERT: A 453 GLN cc_start: 0.7083 (mt0) cc_final: 0.6815 (tt0) REVERT: A 516 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6837 (tt0) REVERT: A 529 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7589 (mp0) REVERT: A 726 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7158 (ptmm) REVERT: A 797 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7398 (mtm110) REVERT: A 956 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6633 (mtt90) REVERT: A 958 GLU cc_start: 0.6893 (mp0) cc_final: 0.6142 (pp20) REVERT: A 968 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 972 LYS cc_start: 0.7870 (tppt) cc_final: 0.7281 (ttpp) REVERT: A 976 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7221 (pmt) REVERT: A 1055 LYS cc_start: 0.8184 (mttt) cc_final: 0.7846 (mmtt) REVERT: B 33 LYS cc_start: 0.7624 (tptt) cc_final: 0.7242 (ttpt) REVERT: B 120 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6956 (mtt) REVERT: B 162 TYR cc_start: 0.8896 (t80) cc_final: 0.8618 (t80) REVERT: B 170 GLU cc_start: 0.7816 (pm20) cc_final: 0.7514 (tm-30) REVERT: B 191 GLN cc_start: 0.8205 (pt0) cc_final: 0.7140 (mm-40) REVERT: B 195 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6509 (pt) REVERT: B 217 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7821 (tm) REVERT: B 233 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5837 (pm20) REVERT: B 351 LYS cc_start: 0.7596 (tppt) cc_final: 0.6817 (mtpt) REVERT: B 434 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6026 (mp10) REVERT: B 438 LYS cc_start: 0.8107 (tttp) cc_final: 0.7360 (ttmt) REVERT: B 529 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: B 539 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7065 (mm-30) REVERT: B 543 GLU cc_start: 0.7542 (pt0) cc_final: 0.7276 (pm20) REVERT: B 608 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: B 635 GLU cc_start: 0.7292 (pp20) cc_final: 0.6905 (pt0) REVERT: B 697 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6675 (ptm-80) REVERT: B 726 LYS cc_start: 0.8017 (mttm) cc_final: 0.7386 (mptp) REVERT: B 739 ASN cc_start: 0.7956 (t0) cc_final: 0.6941 (m-40) REVERT: B 776 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 814 LYS cc_start: 0.8390 (ttpp) cc_final: 0.7992 (tppp) REVERT: B 815 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8291 (mttm) REVERT: B 891 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7886 (mmtm) REVERT: B 956 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7488 (mtp180) REVERT: B 1022 ARG cc_start: 0.6683 (ttp80) cc_final: 0.6129 (ttp80) outliers start: 79 outliers final: 42 residues processed: 278 average time/residue: 0.6972 time to fit residues: 213.1741 Evaluate side-chains 270 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 956 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 5 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 392 HIS A 527 HIS B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128857 restraints weight = 19340.770| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.69 r_work: 0.3345 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17060 Z= 0.128 Angle : 0.519 6.580 23146 Z= 0.263 Chirality : 0.040 0.130 2472 Planarity : 0.004 0.047 2984 Dihedral : 7.738 117.347 2378 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 3.52 % Allowed : 26.62 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.19), residues: 2040 helix: 1.36 (0.17), residues: 908 sheet: -0.39 (0.29), residues: 292 loop : -0.30 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.020 0.001 TYR A 281 PHE 0.019 0.001 PHE B 69 TRP 0.016 0.001 TRP A 98 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (17058) covalent geometry : angle 0.51870 / 0.26 (23146) hydrogen bonds : bond 0.03736 / 2.45 ( 767) hydrogen bonds : angle 4.20788 / 2.98 ( 2256) Misc. bond : bond 0.01153 / 0.61 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 220 time to evaluate : 0.645 Fit side-chains REVERT: A 33 LYS cc_start: 0.7509 (mtpm) cc_final: 0.7140 (mtpt) REVERT: A 58 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7181 (mm-30) REVERT: A 112 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6641 (tpp80) REVERT: A 115 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7345 (mttm) REVERT: A 134 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6708 (mtm-85) REVERT: A 184 ASP cc_start: 0.8320 (t70) cc_final: 0.7926 (t0) REVERT: A 191 GLN cc_start: 0.8302 (mt0) cc_final: 0.7590 (mm-40) REVERT: A 291 LYS cc_start: 0.7407 (mmtt) cc_final: 0.6953 (mtpm) REVERT: A 379 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7230 (ttm170) REVERT: A 453 GLN cc_start: 0.7090 (mt0) cc_final: 0.6808 (tt0) REVERT: A 516 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6835 (tt0) REVERT: A 529 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7616 (mp0) REVERT: A 660 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 726 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7084 (ptmm) REVERT: A 797 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7402 (mtm110) REVERT: A 956 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7015 (mtt90) REVERT: A 958 GLU cc_start: 0.6864 (mp0) cc_final: 0.6295 (pp20) REVERT: A 968 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 972 LYS cc_start: 0.7890 (tppt) cc_final: 0.7322 (ttpp) REVERT: A 976 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7309 (pmt) REVERT: A 1055 LYS cc_start: 0.8192 (mttt) cc_final: 0.7857 (mmtt) REVERT: B 33 LYS cc_start: 0.7607 (tptt) cc_final: 0.7236 (ttpt) REVERT: B 120 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6937 (mtm) REVERT: B 162 TYR cc_start: 0.8916 (t80) cc_final: 0.8692 (t80) REVERT: B 170 GLU cc_start: 0.7856 (pm20) cc_final: 0.7559 (tm-30) REVERT: B 191 GLN cc_start: 0.8222 (pt0) cc_final: 0.7164 (mm-40) REVERT: B 195 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6499 (pt) REVERT: B 217 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7793 (tm) REVERT: B 233 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5721 (pm20) REVERT: B 351 LYS cc_start: 0.7604 (tppt) cc_final: 0.6837 (mtpt) REVERT: B 434 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6013 (mp10) REVERT: B 438 LYS cc_start: 0.8101 (tttp) cc_final: 0.7362 (ttmt) REVERT: B 529 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: B 539 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7044 (mm-30) REVERT: B 543 GLU cc_start: 0.7544 (pt0) cc_final: 0.7278 (pm20) REVERT: B 608 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: B 635 GLU cc_start: 0.7301 (pp20) cc_final: 0.6931 (pt0) REVERT: B 697 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6631 (ptm-80) REVERT: B 703 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8487 (mt-10) REVERT: B 726 LYS cc_start: 0.8034 (mttm) cc_final: 0.7414 (mptp) REVERT: B 739 ASN cc_start: 0.7931 (t0) cc_final: 0.6958 (m110) REVERT: B 776 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: B 814 LYS cc_start: 0.8406 (ttpp) cc_final: 0.7996 (tppp) REVERT: B 815 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8303 (mttm) REVERT: B 891 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7878 (mmtm) REVERT: B 956 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7459 (mtp180) REVERT: B 1022 ARG cc_start: 0.6655 (ttp80) cc_final: 0.6089 (ttp80) outliers start: 62 outliers final: 39 residues processed: 264 average time/residue: 0.7421 time to fit residues: 214.9476 Evaluate side-chains 273 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 956 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 155 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 91 optimal weight: 0.0270 chunk 93 optimal weight: 6.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 392 HIS A 527 HIS B 130 GLN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129049 restraints weight = 19376.218| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.70 r_work: 0.3345 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17060 Z= 0.129 Angle : 0.517 6.715 23146 Z= 0.262 Chirality : 0.040 0.129 2472 Planarity : 0.004 0.045 2984 Dihedral : 7.710 116.406 2378 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 3.41 % Allowed : 26.67 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 2040 helix: 1.39 (0.17), residues: 910 sheet: -0.33 (0.29), residues: 280 loop : -0.32 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 99 TYR 0.020 0.001 TYR A 281 PHE 0.015 0.001 PHE B 160 TRP 0.016 0.001 TRP A 98 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (17058) covalent geometry : angle 0.51735 / 0.26 (23146) hydrogen bonds : bond 0.03723 / 2.44 ( 767) hydrogen bonds : angle 4.19596 / 2.96 ( 2256) Misc. bond : bond 0.01231 / 0.65 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.642 Fit side-chains REVERT: A 33 LYS cc_start: 0.7480 (mtpm) cc_final: 0.7143 (mtpt) REVERT: A 112 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6637 (tpp80) REVERT: A 115 LYS cc_start: 0.7656 (mtpp) cc_final: 0.7337 (mttm) REVERT: A 134 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6640 (mtm-85) REVERT: A 184 ASP cc_start: 0.8317 (t70) cc_final: 0.7925 (t0) REVERT: A 191 GLN cc_start: 0.8302 (mt0) cc_final: 0.7595 (mm-40) REVERT: A 291 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6786 (mtpm) REVERT: A 295 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7267 (mm-30) REVERT: A 453 GLN cc_start: 0.7025 (mt0) cc_final: 0.6782 (tt0) REVERT: A 516 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6814 (tt0) REVERT: A 529 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7560 (mp0) REVERT: A 660 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 726 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7078 (ptmm) REVERT: A 797 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7409 (mtm110) REVERT: A 956 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6977 (mtt90) REVERT: A 958 GLU cc_start: 0.6890 (mp0) cc_final: 0.6137 (pp20) REVERT: A 968 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 972 LYS cc_start: 0.7880 (tppt) cc_final: 0.7305 (ttpp) REVERT: A 976 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7332 (pmt) REVERT: A 1055 LYS cc_start: 0.8214 (mttt) cc_final: 0.7872 (mmtt) REVERT: B 6 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7138 (pp) REVERT: B 33 LYS cc_start: 0.7611 (tptt) cc_final: 0.7221 (ttpt) REVERT: B 120 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6872 (mtm) REVERT: B 162 TYR cc_start: 0.8918 (t80) cc_final: 0.8685 (t80) REVERT: B 170 GLU cc_start: 0.7850 (pm20) cc_final: 0.7470 (tm-30) REVERT: B 191 GLN cc_start: 0.8210 (pt0) cc_final: 0.7184 (mm-40) REVERT: B 195 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6522 (pt) REVERT: B 217 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7776 (tm) REVERT: B 233 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5702 (pm20) REVERT: B 238 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 351 LYS cc_start: 0.7574 (tppt) cc_final: 0.6785 (mtpt) REVERT: B 434 GLN cc_start: 0.6791 (mm-40) cc_final: 0.6000 (mp10) REVERT: B 438 LYS cc_start: 0.8109 (tttp) cc_final: 0.7370 (ttmt) REVERT: B 529 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: B 539 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7057 (mm-30) REVERT: B 543 GLU cc_start: 0.7521 (pt0) cc_final: 0.7264 (pm20) REVERT: B 608 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: B 635 GLU cc_start: 0.7280 (pp20) cc_final: 0.6950 (pt0) REVERT: B 697 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6668 (ptm-80) REVERT: B 726 LYS cc_start: 0.8030 (mttm) cc_final: 0.7420 (mptp) REVERT: B 739 ASN cc_start: 0.7924 (t0) cc_final: 0.6952 (m110) REVERT: B 776 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: B 814 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7972 (tppp) REVERT: B 815 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8301 (mttm) REVERT: B 891 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7874 (mmtm) REVERT: B 956 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: B 1022 ARG cc_start: 0.6639 (ttp80) cc_final: 0.6062 (ttp80) outliers start: 60 outliers final: 38 residues processed: 266 average time/residue: 0.7079 time to fit residues: 206.6178 Evaluate side-chains 272 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 956 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 0.0040 chunk 2 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 392 HIS A 527 HIS B 103 ASN B 392 HIS ** B 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132064 restraints weight = 19379.335| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.66 r_work: 0.3387 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17060 Z= 0.101 Angle : 0.489 6.945 23146 Z= 0.248 Chirality : 0.039 0.134 2472 Planarity : 0.004 0.047 2984 Dihedral : 7.568 114.414 2378 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 2.72 % Allowed : 27.30 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.19), residues: 2040 helix: 1.55 (0.17), residues: 910 sheet: -0.24 (0.29), residues: 278 loop : -0.25 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 99 TYR 0.021 0.001 TYR A 281 PHE 0.019 0.001 PHE B 69 TRP 0.014 0.001 TRP A 98 HIS 0.003 0.001 HIS B 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (17058) covalent geometry : angle 0.48900 / 0.25 (23146) hydrogen bonds : bond 0.03283 / 2.15 ( 767) hydrogen bonds : angle 4.06405 / 2.87 ( 2256) Misc. bond : bond 0.00786 / 0.41 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5940.64 seconds wall clock time: 101 minutes 54.03 seconds (6114.03 seconds total)