Starting phenix.real_space_refine on Sat Feb 24 09:57:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0w_16373/02_2024/8c0w_16373_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0w_16373/02_2024/8c0w_16373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0w_16373/02_2024/8c0w_16373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0w_16373/02_2024/8c0w_16373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0w_16373/02_2024/8c0w_16373_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0w_16373/02_2024/8c0w_16373_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 10 5.21 5 S 195 5.16 5 C 27229 2.51 5 N 7349 2.21 5 O 8275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 903": "OE1" <-> "OE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 999": "OE1" <-> "OE2" Residue "F TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 43092 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8003 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 33} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6215 Classifications: {'peptide': 821} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 29, 'TRANS': 791} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8003 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 33} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6215 Classifications: {'peptide': 821} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 29, 'TRANS': 791} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "E" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8003 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 33} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "F" Number of atoms: 6234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6234 Classifications: {'peptide': 823} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 29, 'TRANS': 793} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 21.51, per 1000 atoms: 0.50 Number of scatterers: 43092 At special positions: 0 Unit cell: (191.08, 185.64, 141.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 195 16.00 P 34 15.00 Mg 10 11.99 O 8275 8.00 N 7349 7.00 C 27229 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.23 Conformation dependent library (CDL) restraints added in 7.8 seconds 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 214 helices and 43 sheets defined 34.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.98 Creating SS restraints... Processing helix chain 'A' and resid 22 through 25 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.022A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.568A pdb=" N SER A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 325 through 339 removed outlier: 3.883A pdb=" N ASN A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.747A pdb=" N ALA A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 429 through 432 No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.901A pdb=" N TYR A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 438' Processing helix chain 'A' and resid 452 through 470 removed outlier: 4.363A pdb=" N SER A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 522 through 534 removed outlier: 4.385A pdb=" N TYR A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 563 through 586 removed outlier: 4.953A pdb=" N LEU A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 604 through 609 removed outlier: 5.081A pdb=" N HIS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.768A pdb=" N LEU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 667 through 689 Processing helix chain 'A' and resid 703 through 720 Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 739 through 753 Proline residue: A 751 - end of helix Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.614A pdb=" N PHE A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 801 No H-bonds generated for 'chain 'A' and resid 799 through 801' Processing helix chain 'A' and resid 809 through 823 removed outlier: 3.741A pdb=" N ASN A 812 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 820 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 836 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.811A pdb=" N VAL A 854 " --> pdb=" O MET A 850 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 3.924A pdb=" N LEU A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 940 through 971 removed outlier: 3.762A pdb=" N LYS A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 981 No H-bonds generated for 'chain 'A' and resid 979 through 981' Processing helix chain 'A' and resid 983 through 986 No H-bonds generated for 'chain 'A' and resid 983 through 986' Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1014 through 1027 removed outlier: 3.976A pdb=" N ASN A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 removed outlier: 3.560A pdb=" N SER B 263 " --> pdb=" O LYS B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 294 through 297 No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.836A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 400 through 406 removed outlier: 4.530A pdb=" N ASP B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.918A pdb=" N ASN B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.986A pdb=" N SER B 498 " --> pdb=" O HIS B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 501 through 516 Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.844A pdb=" N PHE B 531 " --> pdb=" O GLU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 565 removed outlier: 4.240A pdb=" N LEU B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 605 through 618 removed outlier: 4.029A pdb=" N TYR B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 636 Processing helix chain 'B' and resid 642 through 659 Processing helix chain 'B' and resid 670 through 677 removed outlier: 4.194A pdb=" N SER B 676 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 718 removed outlier: 3.793A pdb=" N TRP B 715 " --> pdb=" O GLU B 711 " (cutoff:3.500A) Proline residue: B 716 - end of helix Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.857A pdb=" N VAL B 751 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 752 " --> pdb=" O SER B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 815 through 824 Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'B' and resid 867 through 879 removed outlier: 3.626A pdb=" N ASN B 879 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 904 removed outlier: 4.662A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 939 removed outlier: 4.473A pdb=" N ASP B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Proline residue: B 939 - end of helix Processing helix chain 'B' and resid 957 through 966 removed outlier: 4.060A pdb=" N LEU B 960 " --> pdb=" O GLU B 957 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR B 964 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 996 removed outlier: 4.300A pdb=" N ALA B 996 " --> pdb=" O ASP B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1018 removed outlier: 3.793A pdb=" N TYR B1016 " --> pdb=" O ARG B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.559A pdb=" N HIS C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.393A pdb=" N SER C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 322 No H-bonds generated for 'chain 'C' and resid 320 through 322' Processing helix chain 'C' and resid 325 through 341 removed outlier: 4.181A pdb=" N ASN C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C 330 " --> pdb=" O CYS C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 435 through 438 No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.680A pdb=" N SER C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 499 removed outlier: 3.515A pdb=" N VAL C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 539 removed outlier: 4.215A pdb=" N ASN C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL C 536 " --> pdb=" O LYS C 532 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU C 537 " --> pdb=" O CYS C 533 " (cutoff:3.500A) Proline residue: C 538 - end of helix Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 563 through 586 removed outlier: 3.552A pdb=" N PHE C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 621 through 631 removed outlier: 4.293A pdb=" N ARG C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 640 removed outlier: 5.498A pdb=" N ASP C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 667 through 690 removed outlier: 3.608A pdb=" N LYS C 690 " --> pdb=" O TYR C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 720 removed outlier: 3.947A pdb=" N THR C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 733 No H-bonds generated for 'chain 'C' and resid 731 through 733' Processing helix chain 'C' and resid 738 through 748 Processing helix chain 'C' and resid 780 through 788 Processing helix chain 'C' and resid 808 through 811 No H-bonds generated for 'chain 'C' and resid 808 through 811' Processing helix chain 'C' and resid 813 through 822 Processing helix chain 'C' and resid 833 through 836 No H-bonds generated for 'chain 'C' and resid 833 through 836' Processing helix chain 'C' and resid 849 through 861 Processing helix chain 'C' and resid 880 through 882 No H-bonds generated for 'chain 'C' and resid 880 through 882' Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 927 through 933 Processing helix chain 'C' and resid 940 through 970 removed outlier: 3.771A pdb=" N ASP C 949 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 955 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 966 " --> pdb=" O GLU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 1000 through 1007 Processing helix chain 'C' and resid 1014 through 1026 removed outlier: 4.401A pdb=" N HIS C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR C1020 " --> pdb=" O GLU C1016 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C1023 " --> pdb=" O HIS C1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 removed outlier: 4.224A pdb=" N ALA D 299 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 350 removed outlier: 4.159A pdb=" N LEU D 350 " --> pdb=" O GLN D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.576A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 447 removed outlier: 3.755A pdb=" N LEU D 447 " --> pdb=" O VAL D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 500 through 516 Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 549 through 565 removed outlier: 3.648A pdb=" N PHE D 556 " --> pdb=" O LYS D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 Processing helix chain 'D' and resid 605 through 616 removed outlier: 3.789A pdb=" N ALA D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 610 " --> pdb=" O HIS D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 636 removed outlier: 4.281A pdb=" N GLU D 636 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 657 Processing helix chain 'D' and resid 668 through 675 removed outlier: 3.752A pdb=" N SER D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 675 " --> pdb=" O PHE D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 684 No H-bonds generated for 'chain 'D' and resid 682 through 684' Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 715 through 718 No H-bonds generated for 'chain 'D' and resid 715 through 718' Processing helix chain 'D' and resid 720 through 725 Processing helix chain 'D' and resid 744 through 754 removed outlier: 3.730A pdb=" N SER D 749 " --> pdb=" O THR D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 766 No H-bonds generated for 'chain 'D' and resid 764 through 766' Processing helix chain 'D' and resid 779 through 788 Processing helix chain 'D' and resid 799 through 802 No H-bonds generated for 'chain 'D' and resid 799 through 802' Processing helix chain 'D' and resid 813 through 821 removed outlier: 4.340A pdb=" N GLN D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 877 Processing helix chain 'D' and resid 903 through 908 removed outlier: 4.588A pdb=" N GLY D 907 " --> pdb=" O LYS D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 931 Processing helix chain 'D' and resid 957 through 969 Processing helix chain 'D' and resid 990 through 996 removed outlier: 5.273A pdb=" N LEU D 994 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1007 through 1016 removed outlier: 3.906A pdb=" N TYR D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 Processing helix chain 'E' and resid 70 through 73 No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 119 through 130 Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing helix chain 'E' and resid 216 through 218 No H-bonds generated for 'chain 'E' and resid 216 through 218' Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 282 through 285 No H-bonds generated for 'chain 'E' and resid 282 through 285' Processing helix chain 'E' and resid 320 through 323 No H-bonds generated for 'chain 'E' and resid 320 through 323' Processing helix chain 'E' and resid 325 through 340 removed outlier: 4.616A pdb=" N ASN E 329 " --> pdb=" O CYS E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 381 Processing helix chain 'E' and resid 435 through 438 No H-bonds generated for 'chain 'E' and resid 435 through 438' Processing helix chain 'E' and resid 452 through 464 removed outlier: 3.506A pdb=" N THR E 463 " --> pdb=" O ASN E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 469 No H-bonds generated for 'chain 'E' and resid 466 through 469' Processing helix chain 'E' and resid 489 through 499 removed outlier: 4.002A pdb=" N VAL E 493 " --> pdb=" O LYS E 489 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS E 498 " --> pdb=" O ARG E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 removed outlier: 3.576A pdb=" N LYS E 532 " --> pdb=" O TYR E 528 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 563 through 586 removed outlier: 3.938A pdb=" N THR E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 601 No H-bonds generated for 'chain 'E' and resid 599 through 601' Processing helix chain 'E' and resid 604 through 609 removed outlier: 5.497A pdb=" N HIS E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 632 Processing helix chain 'E' and resid 634 through 638 Processing helix chain 'E' and resid 655 through 659 Processing helix chain 'E' and resid 670 through 688 Processing helix chain 'E' and resid 703 through 716 removed outlier: 3.697A pdb=" N ASN E 715 " --> pdb=" O SER E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 749 removed outlier: 3.992A pdb=" N LEU E 745 " --> pdb=" O LYS E 741 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP E 746 " --> pdb=" O GLY E 742 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR E 747 " --> pdb=" O GLU E 743 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE E 748 " --> pdb=" O ILE E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 778 through 789 removed outlier: 3.525A pdb=" N ALA E 782 " --> pdb=" O LYS E 778 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS E 783 " --> pdb=" O THR E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 822 removed outlier: 3.747A pdb=" N PHE E 817 " --> pdb=" O ARG E 814 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 822 " --> pdb=" O LYS E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 835 No H-bonds generated for 'chain 'E' and resid 833 through 835' Processing helix chain 'E' and resid 854 through 857 No H-bonds generated for 'chain 'E' and resid 854 through 857' Processing helix chain 'E' and resid 860 through 867 Processing helix chain 'E' and resid 880 through 882 No H-bonds generated for 'chain 'E' and resid 880 through 882' Processing helix chain 'E' and resid 908 through 916 Processing helix chain 'E' and resid 929 through 933 Processing helix chain 'E' and resid 941 through 967 Processing helix chain 'E' and resid 969 through 971 No H-bonds generated for 'chain 'E' and resid 969 through 971' Processing helix chain 'E' and resid 979 through 986 removed outlier: 5.117A pdb=" N ASP E 984 " --> pdb=" O ARG E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 996 through 998 No H-bonds generated for 'chain 'E' and resid 996 through 998' Processing helix chain 'E' and resid 1000 through 1007 removed outlier: 4.394A pdb=" N GLN E1007 " --> pdb=" O LYS E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1027 removed outlier: 4.061A pdb=" N ASN E1026 " --> pdb=" O ALA E1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 Processing helix chain 'F' and resid 344 through 350 Processing helix chain 'F' and resid 363 through 365 No H-bonds generated for 'chain 'F' and resid 363 through 365' Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 400 through 409 Processing helix chain 'F' and resid 438 through 448 removed outlier: 4.402A pdb=" N LEU F 447 " --> pdb=" O VAL F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 479 Processing helix chain 'F' and resid 491 through 493 No H-bonds generated for 'chain 'F' and resid 491 through 493' Processing helix chain 'F' and resid 500 through 516 Processing helix chain 'F' and resid 527 through 531 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 549 through 567 removed outlier: 3.610A pdb=" N LYS F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 586 through 590 Processing helix chain 'F' and resid 605 through 618 Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 642 through 658 removed outlier: 3.982A pdb=" N ASP F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU F 656 " --> pdb=" O ILE F 652 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN F 657 " --> pdb=" O PHE F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 674 Processing helix chain 'F' and resid 696 through 698 No H-bonds generated for 'chain 'F' and resid 696 through 698' Processing helix chain 'F' and resid 706 through 718 Proline residue: F 716 - end of helix Processing helix chain 'F' and resid 720 through 722 No H-bonds generated for 'chain 'F' and resid 720 through 722' Processing helix chain 'F' and resid 745 through 753 removed outlier: 4.093A pdb=" N ALA F 750 " --> pdb=" O LEU F 746 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN F 753 " --> pdb=" O SER F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 767 removed outlier: 4.282A pdb=" N ILE F 767 " --> pdb=" O GLY F 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 764 through 767' Processing helix chain 'F' and resid 774 through 787 removed outlier: 3.827A pdb=" N ARG F 780 " --> pdb=" O GLU F 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 824 Processing helix chain 'F' and resid 832 through 834 No H-bonds generated for 'chain 'F' and resid 832 through 834' Processing helix chain 'F' and resid 849 through 851 No H-bonds generated for 'chain 'F' and resid 849 through 851' Processing helix chain 'F' and resid 867 through 879 Processing helix chain 'F' and resid 899 through 903 removed outlier: 3.522A pdb=" N GLU F 903 " --> pdb=" O LEU F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 916 No H-bonds generated for 'chain 'F' and resid 914 through 916' Processing helix chain 'F' and resid 920 through 929 removed outlier: 3.549A pdb=" N ARG F 927 " --> pdb=" O LYS F 923 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP F 928 " --> pdb=" O SER F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 932 through 936 Processing helix chain 'F' and resid 990 through 998 Processing helix chain 'F' and resid 1006 through 1019 removed outlier: 4.549A pdb=" N LYS F1011 " --> pdb=" O SER F1007 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F1014 " --> pdb=" O VAL F1010 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F1019 " --> pdb=" O ILE F1015 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 84 through 86 Processing sheet with id= B, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.778A pdb=" N LEU A 34 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 100 through 106 removed outlier: 5.787A pdb=" N GLN A 169 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE A 103 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 171 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE A 105 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 173 " --> pdb=" O ILE A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 138 through 140 Processing sheet with id= E, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= F, first strand: chain 'A' and resid 206 through 209 Processing sheet with id= G, first strand: chain 'A' and resid 250 through 253 Processing sheet with id= H, first strand: chain 'A' and resid 351 through 356 Processing sheet with id= I, first strand: chain 'A' and resid 478 through 481 removed outlier: 6.495A pdb=" N LEU A 505 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA A 548 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A 507 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 767 through 770 removed outlier: 6.314A pdb=" N VAL A 873 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE A 770 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 875 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN A 792 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 829 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 794 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 831 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 796 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.189A pdb=" N LEU B 292 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N HIS B 289 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER B 236 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 233 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE B 278 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE B 235 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS B 280 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS B 245 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 316 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU B 210 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 392 through 394 Processing sheet with id= M, first strand: chain 'B' and resid 355 through 357 removed outlier: 3.572A pdb=" N LEU B 356 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 597 through 599 removed outlier: 8.837A pdb=" N TRP B 598 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 458 " --> pdb=" O TRP B 598 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 574 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU B 459 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE B 576 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE B 485 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 523 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 487 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASP B 525 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA B 489 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 860 through 862 removed outlier: 3.537A pdb=" N VAL B 860 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 836 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 736 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 838 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLY B 738 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 840 " --> pdb=" O GLY B 738 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 835 " --> pdb=" O CYS B 792 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B 758 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE B 795 " --> pdb=" O ASN B 758 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 760 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 65 through 69 removed outlier: 8.451A pdb=" N ILE C 66 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER C 4 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 68 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 6 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 16 through 19 Processing sheet with id= R, first strand: chain 'C' and resid 171 through 175 removed outlier: 5.499A pdb=" N LEU C 104 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 152 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 138 through 140 removed outlier: 3.530A pdb=" N GLY C 161 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 203 through 206 Processing sheet with id= U, first strand: chain 'C' and resid 207 through 209 removed outlier: 6.046A pdb=" N ILE C 278 " --> pdb=" O GLU C 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 232 through 235 removed outlier: 6.183A pdb=" N LYS C 263 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR C 235 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE C 265 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER C 249 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 351 through 356 Processing sheet with id= X, first strand: chain 'C' and resid 612 through 615 removed outlier: 6.686A pdb=" N HIS C 503 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 546 " --> pdb=" O HIS C 503 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU C 505 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA C 548 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE C 507 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 896 through 898 removed outlier: 7.978A pdb=" N LEU C 897 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 769 " --> pdb=" O LEU C 897 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 873 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N PHE C 770 " --> pdb=" O VAL C 873 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY C 875 " --> pdb=" O PHE C 770 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE C 874 " --> pdb=" O CYS C 826 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE C 828 " --> pdb=" O ILE C 874 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA C 876 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE C 830 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN C 792 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE C 829 " --> pdb=" O ASN C 792 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE C 794 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASP C 831 " --> pdb=" O PHE C 794 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL C 796 " --> pdb=" O ASP C 831 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 214 through 216 Processing sheet with id= AA, first strand: chain 'D' and resid 290 through 292 removed outlier: 3.554A pdb=" N ALA D 291 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 234 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS D 280 " --> pdb=" O ILE D 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 456 through 460 removed outlier: 8.749A pdb=" N ILE D 457 " --> pdb=" O ILE D 572 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 574 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU D 459 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE D 576 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D 520 " --> pdb=" O ARG D 573 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU D 575 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 522 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N SER D 577 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU D 524 " --> pdb=" O SER D 577 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE D 485 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 523 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS D 487 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP D 525 " --> pdb=" O LYS D 487 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA D 489 " --> pdb=" O ASP D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 734 through 736 removed outlier: 3.529A pdb=" N LEU D 837 " --> pdb=" O LEU D 794 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 65 through 69 removed outlier: 8.794A pdb=" N ILE E 66 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER E 4 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 68 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 6 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 34 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS E 16 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASP E 58 " --> pdb=" O CYS E 16 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE E 18 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 169 through 173 Processing sheet with id= AF, first strand: chain 'E' and resid 138 through 140 Processing sheet with id= AG, first strand: chain 'E' and resid 207 through 209 removed outlier: 5.953A pdb=" N ILE E 278 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LYS E 263 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR E 235 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE E 265 " --> pdb=" O THR E 235 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 251 through 254 Processing sheet with id= AI, first strand: chain 'E' and resid 314 through 316 removed outlier: 3.555A pdb=" N ASP E 350 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 344 through 347 Processing sheet with id= AK, first strand: chain 'E' and resid 612 through 615 removed outlier: 3.849A pdb=" N ALA E 476 " --> pdb=" O THR E 590 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA E 543 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL E 593 " --> pdb=" O ALA E 543 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 545 " --> pdb=" O VAL E 593 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N SER E 595 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU E 547 " --> pdb=" O SER E 595 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 769 through 772 Processing sheet with id= AM, first strand: chain 'F' and resid 289 through 291 removed outlier: 8.265A pdb=" N ILE F 290 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG F 217 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE F 314 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS F 213 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU F 312 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE F 215 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE F 310 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS F 245 " --> pdb=" O LEU F 315 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 391 through 397 removed outlier: 6.693A pdb=" N ALA F 328 " --> pdb=" O GLN F 392 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LYS F 394 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL F 330 " --> pdb=" O LYS F 394 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR F 396 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE F 332 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 355 through 357 Processing sheet with id= AP, first strand: chain 'F' and resid 597 through 599 removed outlier: 8.636A pdb=" N TRP F 598 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE F 458 " --> pdb=" O TRP F 598 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ILE F 457 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL F 574 " --> pdb=" O ILE F 457 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU F 459 " --> pdb=" O VAL F 574 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE F 576 " --> pdb=" O LEU F 459 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER F 520 " --> pdb=" O ARG F 573 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LEU F 575 " --> pdb=" O SER F 520 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE F 522 " --> pdb=" O LEU F 575 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER F 577 " --> pdb=" O ILE F 522 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU F 524 " --> pdb=" O SER F 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'F' and resid 735 through 738 1192 hydrogen bonds defined for protein. 2940 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: 16.32 Time building geometry restraints manager: 17.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11697 1.33 - 1.45: 7634 1.45 - 1.58: 24271 1.58 - 1.70: 31 1.70 - 1.82: 288 Bond restraints: 43921 Sorted by residual: bond pdb=" CB GLN C 124 " pdb=" CG GLN C 124 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.56e+00 bond pdb=" CG1 ILE B 734 " pdb=" CD1 ILE B 734 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.87e+00 bond pdb=" CG1 ILE E 744 " pdb=" CD1 ILE E 744 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.65e+00 bond pdb=" CG1 ILE E 627 " pdb=" CD1 ILE E 627 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.69e+00 bond pdb=" CG LEU B 521 " pdb=" CD2 LEU B 521 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.69e+00 ... (remaining 43916 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.96: 1107 105.96 - 114.43: 25722 114.43 - 122.90: 28643 122.90 - 131.37: 3848 131.37 - 139.84: 88 Bond angle restraints: 59408 Sorted by residual: angle pdb=" C ARG A 639 " pdb=" N ASP A 640 " pdb=" CA ASP A 640 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.03e+01 angle pdb=" C ALA C 361 " pdb=" CA ALA C 361 " pdb=" CB ALA C 361 " ideal model delta sigma weight residual 116.54 109.36 7.18 1.15e+00 7.56e-01 3.90e+01 angle pdb=" CA GLN C 124 " pdb=" CB GLN C 124 " pdb=" CG GLN C 124 " ideal model delta sigma weight residual 114.10 124.62 -10.52 2.00e+00 2.50e-01 2.77e+01 angle pdb=" C ARG E 917 " pdb=" N LYS E 918 " pdb=" CA LYS E 918 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ARG E 413 " pdb=" CA ARG E 413 " pdb=" C ARG E 413 " ideal model delta sigma weight residual 108.00 115.36 -7.36 1.48e+00 4.57e-01 2.48e+01 ... (remaining 59403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 25702 31.02 - 62.04: 577 62.04 - 93.06: 126 93.06 - 124.08: 4 124.08 - 155.10: 2 Dihedral angle restraints: 26411 sinusoidal: 10779 harmonic: 15632 Sorted by residual: dihedral pdb=" O2A ADP D1102 " pdb=" O3A ADP D1102 " pdb=" PA ADP D1102 " pdb=" PB ADP D1102 " ideal model delta sinusoidal sigma weight residual 300.00 144.90 155.10 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP F1102 " pdb=" O3A ADP F1102 " pdb=" PA ADP F1102 " pdb=" PB ADP F1102 " ideal model delta sinusoidal sigma weight residual -60.00 86.58 -146.58 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" C4' ADP D1102 " pdb=" C5' ADP D1102 " pdb=" O5' ADP D1102 " pdb=" PA ADP D1102 " ideal model delta sinusoidal sigma weight residual -180.00 -59.44 -120.56 1 2.00e+01 2.50e-03 3.62e+01 ... (remaining 26408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5964 0.087 - 0.174: 626 0.174 - 0.261: 16 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CG LEU A 512 " pdb=" CB LEU A 512 " pdb=" CD1 LEU A 512 " pdb=" CD2 LEU A 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB ILE B 734 " pdb=" CA ILE B 734 " pdb=" CG1 ILE B 734 " pdb=" CG2 ILE B 734 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLN C 124 " pdb=" N GLN C 124 " pdb=" C GLN C 124 " pdb=" CB GLN C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 6605 not shown) Planarity restraints: 7665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 624 " -0.361 9.50e-02 1.11e+02 1.63e-01 1.93e+01 pdb=" NE ARG C 624 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 624 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG C 624 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 624 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 892 " 0.334 9.50e-02 1.11e+02 1.50e-01 1.61e+01 pdb=" NE ARG E 892 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG E 892 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG E 892 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 892 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 469 " 0.288 9.50e-02 1.11e+02 1.30e-01 1.29e+01 pdb=" NE ARG B 469 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 469 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 469 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 469 " 0.001 2.00e-02 2.50e+03 ... (remaining 7662 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 132 2.38 - 3.01: 26232 3.01 - 3.64: 65176 3.64 - 4.27: 92663 4.27 - 4.90: 145133 Nonbonded interactions: 329336 Sorted by model distance: nonbonded pdb=" O1B ATP B1101 " pdb="MG MG B1103 " model vdw 1.748 2.170 nonbonded pdb=" O1B ATP A1101 " pdb="MG MG A1103 " model vdw 1.755 2.170 nonbonded pdb=" O3B ATP B1102 " pdb="MG MG B1104 " model vdw 1.776 2.170 nonbonded pdb=" O3G ATP B1101 " pdb="MG MG B1103 " model vdw 1.800 2.170 nonbonded pdb=" O2B ATP D1101 " pdb="MG MG D1103 " model vdw 1.815 2.170 ... (remaining 329331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 201 through 1021) selection = (chain 'D' and resid 201 through 1021) selection = (chain 'F' and resid 201 through 1021) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 14.030 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 107.660 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 0.077 43921 Z= 0.286 Angle : 0.888 13.546 59408 Z= 0.491 Chirality : 0.052 0.435 6608 Planarity : 0.009 0.163 7665 Dihedral : 14.885 155.102 16483 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.10), residues: 5543 helix: -1.79 (0.10), residues: 1711 sheet: -0.96 (0.20), residues: 651 loop : -1.91 (0.11), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 510 HIS 0.019 0.001 HIS D 808 PHE 0.050 0.002 PHE C 583 TYR 0.036 0.005 TYR A 539 ARG 0.031 0.004 ARG C 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 5.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.6607 (m-80) cc_final: 0.6325 (m-80) REVERT: A 108 GLN cc_start: 0.9159 (mt0) cc_final: 0.8759 (tm-30) REVERT: A 120 MET cc_start: 0.7279 (tpt) cc_final: 0.6766 (tpt) REVERT: A 591 THR cc_start: 0.8798 (m) cc_final: 0.8566 (p) REVERT: A 610 MET cc_start: 0.9025 (mmt) cc_final: 0.8822 (mmm) REVERT: A 679 MET cc_start: 0.8872 (ttp) cc_final: 0.8616 (tmm) REVERT: A 781 MET cc_start: 0.9214 (ppp) cc_final: 0.8842 (ppp) REVERT: B 366 GLN cc_start: 0.7871 (mt0) cc_final: 0.7171 (mm-40) REVERT: B 398 MET cc_start: 0.3408 (mmt) cc_final: 0.2456 (mmt) REVERT: B 475 ILE cc_start: 0.9140 (mt) cc_final: 0.8931 (mt) REVERT: B 809 ASP cc_start: 0.6440 (m-30) cc_final: 0.6173 (m-30) REVERT: B 835 TYR cc_start: 0.8345 (m-80) cc_final: 0.8077 (m-10) REVERT: B 850 LEU cc_start: 0.8803 (tp) cc_final: 0.8073 (tp) REVERT: B 888 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7704 (pttt) REVERT: C 244 ASP cc_start: 0.7918 (m-30) cc_final: 0.7613 (t0) REVERT: C 360 MET cc_start: 0.8949 (mmm) cc_final: 0.8608 (mmt) REVERT: C 457 LEU cc_start: 0.9582 (tt) cc_final: 0.9091 (mm) REVERT: C 570 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8834 (tptt) REVERT: C 610 MET cc_start: 0.7842 (ptp) cc_final: 0.7240 (ptp) REVERT: C 746 ASP cc_start: 0.5974 (m-30) cc_final: 0.5457 (m-30) REVERT: C 780 LEU cc_start: 0.9343 (tp) cc_final: 0.9083 (tt) REVERT: C 805 TYR cc_start: 0.7501 (m-80) cc_final: 0.7035 (m-10) REVERT: C 829 PHE cc_start: 0.8854 (t80) cc_final: 0.8316 (t80) REVERT: C 874 ILE cc_start: 0.9571 (pt) cc_final: 0.9326 (pt) REVERT: C 971 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6377 (tt0) REVERT: C 1008 LEU cc_start: 0.8432 (tp) cc_final: 0.7982 (tp) REVERT: D 317 MET cc_start: 0.7978 (tpt) cc_final: 0.7710 (tpt) REVERT: D 837 LEU cc_start: 0.8044 (tp) cc_final: 0.7552 (tp) REVERT: E 1 MET cc_start: 0.8070 (ppp) cc_final: 0.7628 (tpp) REVERT: E 376 ASP cc_start: 0.8287 (m-30) cc_final: 0.7918 (p0) REVERT: E 533 CYS cc_start: 0.8311 (m) cc_final: 0.7951 (m) REVERT: E 549 HIS cc_start: 0.8413 (m90) cc_final: 0.8151 (m90) REVERT: E 805 TYR cc_start: 0.8019 (t80) cc_final: 0.7689 (m-80) REVERT: E 951 MET cc_start: 0.8198 (tmm) cc_final: 0.7976 (tmm) REVERT: E 961 MET cc_start: 0.8898 (mtp) cc_final: 0.7484 (tmm) REVERT: E 995 VAL cc_start: 0.5060 (t) cc_final: 0.4559 (t) REVERT: F 278 PHE cc_start: 0.7296 (m-80) cc_final: 0.7037 (m-80) REVERT: F 290 ILE cc_start: 0.9371 (mt) cc_final: 0.9168 (mm) REVERT: F 317 MET cc_start: 0.5143 (tpp) cc_final: 0.3954 (mmt) REVERT: F 345 ASP cc_start: 0.6689 (m-30) cc_final: 0.6231 (t70) REVERT: F 381 CYS cc_start: 0.7528 (t) cc_final: 0.7219 (m) REVERT: F 383 LEU cc_start: 0.7710 (mt) cc_final: 0.7191 (tp) REVERT: F 474 LEU cc_start: 0.9550 (tp) cc_final: 0.9185 (tp) REVERT: F 635 LEU cc_start: 0.8818 (mm) cc_final: 0.8536 (tp) REVERT: F 661 ASP cc_start: 0.8256 (m-30) cc_final: 0.7336 (t0) REVERT: F 795 PHE cc_start: 0.8456 (t80) cc_final: 0.7401 (t80) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.6086 time to fit residues: 733.3879 Evaluate side-chains 347 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 5.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 468 optimal weight: 30.0000 chunk 420 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 435 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 chunk 504 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 154 ASN A 535 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 HIS B 284 GLN B 295 HIS B 495 HIS B 566 ASN B 758 ASN B 820 GLN B 824 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN C 535 ASN C 635 HIS C 818 GLN D 295 HIS D 327 ASN D 483 HIS D 625 ASN D 753 GLN E 311 GLN E 384 ASN E 569 GLN E 573 ASN E 643 GLN ** E 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN ** F 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 43921 Z= 0.241 Angle : 0.728 11.575 59408 Z= 0.381 Chirality : 0.046 0.214 6608 Planarity : 0.005 0.055 7665 Dihedral : 11.801 142.476 6286 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.89 % Favored : 93.09 % Rotamer: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.11), residues: 5543 helix: -0.71 (0.12), residues: 1728 sheet: -0.96 (0.19), residues: 661 loop : -1.44 (0.11), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 715 HIS 0.012 0.001 HIS B 495 PHE 0.027 0.002 PHE A 339 TYR 0.024 0.002 TYR E 128 ARG 0.009 0.001 ARG C 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 467 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.6382 (m-80) cc_final: 0.5891 (m-80) REVERT: A 108 GLN cc_start: 0.9133 (mt0) cc_final: 0.8825 (tm-30) REVERT: A 135 MET cc_start: 0.7782 (mmm) cc_final: 0.7472 (mmm) REVERT: A 158 PHE cc_start: 0.8398 (m-80) cc_final: 0.8181 (m-80) REVERT: A 234 PHE cc_start: 0.7858 (p90) cc_final: 0.7436 (p90) REVERT: A 407 PHE cc_start: 0.7557 (p90) cc_final: 0.6962 (p90) REVERT: A 591 THR cc_start: 0.8745 (m) cc_final: 0.8509 (p) REVERT: A 610 MET cc_start: 0.9055 (mmt) cc_final: 0.8588 (mmp) REVERT: A 632 LEU cc_start: 0.9470 (mt) cc_final: 0.9051 (tp) REVERT: A 679 MET cc_start: 0.8935 (ttp) cc_final: 0.8570 (tmm) REVERT: A 781 MET cc_start: 0.9179 (ppp) cc_final: 0.8736 (ppp) REVERT: A 797 LYS cc_start: 0.8218 (tttt) cc_final: 0.7874 (tttm) REVERT: B 366 GLN cc_start: 0.8152 (mt0) cc_final: 0.7324 (mm-40) REVERT: B 398 MET cc_start: 0.3359 (mmt) cc_final: 0.2880 (mmm) REVERT: B 475 ILE cc_start: 0.9206 (mt) cc_final: 0.8826 (mt) REVERT: B 709 LEU cc_start: 0.9500 (mm) cc_final: 0.9296 (mm) REVERT: B 719 TYR cc_start: 0.7928 (m-10) cc_final: 0.7663 (m-10) REVERT: B 835 TYR cc_start: 0.8442 (m-80) cc_final: 0.8037 (m-10) REVERT: B 888 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7644 (pttt) REVERT: B 1021 LYS cc_start: 0.7083 (tttt) cc_final: 0.6147 (mptt) REVERT: C 124 GLN cc_start: 0.8153 (mp10) cc_final: 0.7826 (pt0) REVERT: C 244 ASP cc_start: 0.7656 (m-30) cc_final: 0.7371 (t0) REVERT: C 256 MET cc_start: 0.7591 (pmm) cc_final: 0.7369 (pmm) REVERT: C 360 MET cc_start: 0.8857 (mmm) cc_final: 0.8300 (mmt) REVERT: C 457 LEU cc_start: 0.9505 (tt) cc_final: 0.9163 (mm) REVERT: C 570 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8806 (tptt) REVERT: C 610 MET cc_start: 0.7766 (ptp) cc_final: 0.7337 (ptp) REVERT: C 734 ILE cc_start: 0.7709 (mp) cc_final: 0.7486 (mp) REVERT: C 805 TYR cc_start: 0.7509 (m-80) cc_final: 0.7256 (m-10) REVERT: C 829 PHE cc_start: 0.8848 (t80) cc_final: 0.8411 (t80) REVERT: C 874 ILE cc_start: 0.9622 (pt) cc_final: 0.9273 (mp) REVERT: C 971 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6316 (tt0) REVERT: D 508 MET cc_start: 0.8437 (tmm) cc_final: 0.8079 (tmm) REVERT: D 574 VAL cc_start: 0.9633 (t) cc_final: 0.9397 (p) REVERT: D 622 MET cc_start: 0.8970 (ppp) cc_final: 0.7912 (ppp) REVERT: D 711 GLU cc_start: 0.8320 (tt0) cc_final: 0.8072 (tt0) REVERT: D 825 MET cc_start: 0.7278 (mpp) cc_final: 0.7067 (mpp) REVERT: E 376 ASP cc_start: 0.8287 (m-30) cc_final: 0.7885 (p0) REVERT: E 510 LEU cc_start: 0.7693 (tp) cc_final: 0.7490 (tp) REVERT: E 511 SER cc_start: 0.8809 (m) cc_final: 0.8561 (t) REVERT: E 791 LEU cc_start: 0.7932 (mt) cc_final: 0.7621 (tp) REVERT: E 801 LEU cc_start: 0.6559 (tp) cc_final: 0.5921 (tt) REVERT: E 805 TYR cc_start: 0.7956 (t80) cc_final: 0.7680 (m-80) REVERT: E 812 ASN cc_start: 0.7277 (m-40) cc_final: 0.7043 (m-40) REVERT: E 851 ASP cc_start: 0.9008 (p0) cc_final: 0.8420 (t70) REVERT: E 961 MET cc_start: 0.8839 (mtp) cc_final: 0.7554 (tmm) REVERT: F 317 MET cc_start: 0.5251 (tpp) cc_final: 0.4028 (mmt) REVERT: F 474 LEU cc_start: 0.9424 (tp) cc_final: 0.9194 (tp) REVERT: F 635 LEU cc_start: 0.8725 (mm) cc_final: 0.8452 (tp) REVERT: F 661 ASP cc_start: 0.8318 (m-30) cc_final: 0.7195 (t0) REVERT: F 777 GLN cc_start: 0.8574 (mt0) cc_final: 0.8369 (tm-30) REVERT: F 825 MET cc_start: 0.4571 (tmm) cc_final: 0.4313 (tmm) outliers start: 8 outliers final: 3 residues processed: 474 average time/residue: 0.5188 time to fit residues: 411.9228 Evaluate side-chains 298 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 295 time to evaluate : 4.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 280 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 419 optimal weight: 4.9990 chunk 343 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 504 optimal weight: 4.9990 chunk 545 optimal weight: 6.9990 chunk 449 optimal weight: 20.0000 chunk 500 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 405 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 295 HIS B 758 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 HIS D 359 ASN ** E 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 384 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43921 Z= 0.244 Angle : 0.682 11.417 59408 Z= 0.355 Chirality : 0.045 0.213 6608 Planarity : 0.004 0.056 7665 Dihedral : 11.259 136.214 6286 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 5543 helix: -0.54 (0.12), residues: 1715 sheet: -1.01 (0.19), residues: 663 loop : -1.37 (0.12), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 715 HIS 0.010 0.001 HIS D 808 PHE 0.023 0.002 PHE E 872 TYR 0.025 0.002 TYR C 438 ARG 0.009 0.001 ARG A 981 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 417 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9135 (mt0) cc_final: 0.8828 (tm-30) REVERT: A 135 MET cc_start: 0.7881 (mmm) cc_final: 0.7630 (mmm) REVERT: A 234 PHE cc_start: 0.8126 (p90) cc_final: 0.7714 (p90) REVERT: A 407 PHE cc_start: 0.7566 (p90) cc_final: 0.6978 (p90) REVERT: A 464 SER cc_start: 0.9154 (m) cc_final: 0.8860 (p) REVERT: A 610 MET cc_start: 0.9122 (mmt) cc_final: 0.8696 (mmm) REVERT: A 632 LEU cc_start: 0.9475 (mt) cc_final: 0.9048 (tp) REVERT: A 679 MET cc_start: 0.8906 (ttp) cc_final: 0.8506 (tmm) REVERT: A 781 MET cc_start: 0.9185 (ppp) cc_final: 0.8742 (ppp) REVERT: A 808 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7127 (tm-30) REVERT: A 951 MET cc_start: 0.6671 (ppp) cc_final: 0.6456 (ppp) REVERT: B 366 GLN cc_start: 0.8097 (mt0) cc_final: 0.7161 (mm-40) REVERT: B 398 MET cc_start: 0.3476 (mmt) cc_final: 0.2857 (mmt) REVERT: B 709 LEU cc_start: 0.9514 (mm) cc_final: 0.9283 (mm) REVERT: B 719 TYR cc_start: 0.8016 (m-10) cc_final: 0.7739 (m-10) REVERT: B 825 MET cc_start: 0.7532 (ttp) cc_final: 0.6765 (tmm) REVERT: B 835 TYR cc_start: 0.8437 (m-80) cc_final: 0.7972 (m-10) REVERT: B 888 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7579 (tttt) REVERT: C 244 ASP cc_start: 0.7668 (m-30) cc_final: 0.7314 (t0) REVERT: C 256 MET cc_start: 0.7697 (pmm) cc_final: 0.7442 (pmm) REVERT: C 360 MET cc_start: 0.8816 (mmm) cc_final: 0.8395 (mmm) REVERT: C 457 LEU cc_start: 0.9519 (tt) cc_final: 0.9237 (mm) REVERT: C 492 MET cc_start: 0.9146 (mtp) cc_final: 0.8841 (mtp) REVERT: C 570 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8827 (tptt) REVERT: C 829 PHE cc_start: 0.8741 (t80) cc_final: 0.8439 (t80) REVERT: C 874 ILE cc_start: 0.9616 (pt) cc_final: 0.9270 (mp) REVERT: C 971 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6329 (tt0) REVERT: D 216 LEU cc_start: 0.9149 (tp) cc_final: 0.8897 (tp) REVERT: D 223 MET cc_start: 0.7263 (mmm) cc_final: 0.7030 (mmm) REVERT: D 574 VAL cc_start: 0.9656 (t) cc_final: 0.9449 (p) REVERT: D 622 MET cc_start: 0.9087 (ppp) cc_final: 0.7992 (ppp) REVERT: D 684 ARG cc_start: 0.7630 (mpp80) cc_final: 0.7275 (ttm170) REVERT: D 715 TRP cc_start: 0.7997 (m-10) cc_final: 0.7689 (m-10) REVERT: D 899 LYS cc_start: 0.5886 (tptt) cc_final: 0.5600 (tptm) REVERT: E 1 MET cc_start: 0.7922 (ppp) cc_final: 0.7653 (tpp) REVERT: E 376 ASP cc_start: 0.8402 (m-30) cc_final: 0.7930 (p0) REVERT: E 458 VAL cc_start: 0.9322 (t) cc_final: 0.9118 (p) REVERT: E 511 SER cc_start: 0.8823 (m) cc_final: 0.8589 (t) REVERT: E 805 TYR cc_start: 0.7955 (t80) cc_final: 0.7393 (m-80) REVERT: E 851 ASP cc_start: 0.9009 (p0) cc_final: 0.8391 (t70) REVERT: E 951 MET cc_start: 0.7760 (tmm) cc_final: 0.7185 (ttt) REVERT: E 961 MET cc_start: 0.8894 (mtp) cc_final: 0.7665 (tmm) REVERT: F 317 MET cc_start: 0.5343 (tpp) cc_final: 0.3826 (mmt) REVERT: F 473 GLU cc_start: 0.8068 (tp30) cc_final: 0.7663 (tp30) REVERT: F 635 LEU cc_start: 0.8645 (mm) cc_final: 0.8360 (tp) outliers start: 7 outliers final: 2 residues processed: 423 average time/residue: 0.5312 time to fit residues: 384.0489 Evaluate side-chains 278 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 498 optimal weight: 2.9990 chunk 379 optimal weight: 20.0000 chunk 262 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 chunk 506 optimal weight: 9.9990 chunk 536 optimal weight: 30.0000 chunk 264 optimal weight: 4.9990 chunk 480 optimal weight: 0.1980 chunk 144 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN A 969 HIS B 284 GLN B 295 HIS B 758 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN E 842 ASN ** E 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 976 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43921 Z= 0.171 Angle : 0.636 11.931 59408 Z= 0.327 Chirality : 0.044 0.202 6608 Planarity : 0.004 0.052 7665 Dihedral : 10.793 135.007 6286 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5543 helix: -0.24 (0.12), residues: 1700 sheet: -0.97 (0.19), residues: 698 loop : -1.31 (0.12), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 516 HIS 0.007 0.001 HIS D 808 PHE 0.027 0.001 PHE D 593 TYR 0.026 0.001 TYR F 247 ARG 0.005 0.000 ARG D1013 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 4.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9140 (mt0) cc_final: 0.8828 (tm-30) REVERT: A 135 MET cc_start: 0.7825 (mmm) cc_final: 0.7584 (mmm) REVERT: A 234 PHE cc_start: 0.8188 (p90) cc_final: 0.7684 (p90) REVERT: A 464 SER cc_start: 0.9132 (m) cc_final: 0.8895 (p) REVERT: A 610 MET cc_start: 0.9017 (mmt) cc_final: 0.8623 (mmp) REVERT: A 632 LEU cc_start: 0.9425 (mt) cc_final: 0.9039 (tp) REVERT: A 781 MET cc_start: 0.9158 (ppp) cc_final: 0.8670 (ppp) REVERT: A 808 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7063 (tm-30) REVERT: A 951 MET cc_start: 0.6634 (ppp) cc_final: 0.6427 (ppp) REVERT: B 297 TRP cc_start: 0.7558 (m100) cc_final: 0.7325 (m100) REVERT: B 366 GLN cc_start: 0.8119 (mt0) cc_final: 0.7167 (mm-40) REVERT: B 398 MET cc_start: 0.3310 (mmt) cc_final: 0.2733 (mmt) REVERT: B 622 MET cc_start: 0.7455 (tpt) cc_final: 0.7209 (mmm) REVERT: B 719 TYR cc_start: 0.7849 (m-10) cc_final: 0.7558 (m-10) REVERT: B 825 MET cc_start: 0.7802 (ptt) cc_final: 0.7220 (ttp) REVERT: B 835 TYR cc_start: 0.8435 (m-80) cc_final: 0.7944 (m-10) REVERT: B 888 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7527 (tttt) REVERT: C 114 MET cc_start: 0.2890 (mmm) cc_final: 0.2224 (mtm) REVERT: C 244 ASP cc_start: 0.7654 (m-30) cc_final: 0.7331 (t0) REVERT: C 256 MET cc_start: 0.7652 (pmm) cc_final: 0.7400 (pmm) REVERT: C 457 LEU cc_start: 0.9511 (tt) cc_final: 0.9265 (mm) REVERT: C 492 MET cc_start: 0.9189 (mtp) cc_final: 0.8892 (mtp) REVERT: C 570 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8828 (tptt) REVERT: C 805 TYR cc_start: 0.7628 (m-10) cc_final: 0.7368 (m-10) REVERT: C 829 PHE cc_start: 0.8742 (t80) cc_final: 0.8484 (t80) REVERT: C 874 ILE cc_start: 0.9611 (pt) cc_final: 0.9248 (mp) REVERT: C 971 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6204 (tt0) REVERT: D 317 MET cc_start: 0.7308 (mmm) cc_final: 0.7036 (tpp) REVERT: D 514 CYS cc_start: 0.9134 (m) cc_final: 0.8647 (p) REVERT: D 574 VAL cc_start: 0.9634 (t) cc_final: 0.9430 (p) REVERT: D 622 MET cc_start: 0.9063 (ppp) cc_final: 0.7970 (ppp) REVERT: E 120 MET cc_start: 0.7778 (tpp) cc_final: 0.7284 (tpp) REVERT: E 376 ASP cc_start: 0.8410 (m-30) cc_final: 0.7984 (p0) REVERT: E 463 THR cc_start: 0.9231 (t) cc_final: 0.9019 (p) REVERT: E 510 LEU cc_start: 0.7906 (tp) cc_final: 0.7529 (tp) REVERT: E 511 SER cc_start: 0.8788 (m) cc_final: 0.8540 (t) REVERT: E 851 ASP cc_start: 0.9025 (p0) cc_final: 0.8436 (t70) REVERT: E 951 MET cc_start: 0.7467 (tmm) cc_final: 0.7198 (ttt) REVERT: E 961 MET cc_start: 0.8912 (mtp) cc_final: 0.7771 (tmm) REVERT: F 278 PHE cc_start: 0.7318 (m-80) cc_final: 0.6932 (m-80) REVERT: F 317 MET cc_start: 0.5377 (tpp) cc_final: 0.3777 (mmt) REVERT: F 443 MET cc_start: 0.8972 (mmt) cc_final: 0.8689 (mmt) REVERT: F 635 LEU cc_start: 0.8572 (mm) cc_final: 0.8274 (tp) REVERT: F 1016 TYR cc_start: 0.6726 (m-10) cc_final: 0.5971 (m-80) outliers start: 2 outliers final: 1 residues processed: 431 average time/residue: 0.4917 time to fit residues: 363.1402 Evaluate side-chains 283 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 446 optimal weight: 40.0000 chunk 304 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 399 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 457 optimal weight: 30.0000 chunk 370 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 overall best weight: 15.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 792 ASN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 758 ASN C 369 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 ASN C 629 GLN C 842 ASN C 937 ASN C1005 GLN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 GLN D 967 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN ** E 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 754 HIS E 832 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 43921 Z= 0.616 Angle : 1.068 19.942 59408 Z= 0.556 Chirality : 0.055 0.274 6608 Planarity : 0.008 0.137 7665 Dihedral : 12.100 134.764 6286 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 30.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.51 % Favored : 88.44 % Rotamer: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.10), residues: 5543 helix: -1.63 (0.11), residues: 1722 sheet: -1.59 (0.19), residues: 663 loop : -2.07 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP F 516 HIS 0.021 0.003 HIS E 635 PHE 0.052 0.004 PHE E 628 TYR 0.047 0.004 TYR E 631 ARG 0.030 0.001 ARG F 961 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9240 (mt0) cc_final: 0.9005 (tm-30) REVERT: A 135 MET cc_start: 0.8402 (mmm) cc_final: 0.8085 (mmm) REVERT: A 234 PHE cc_start: 0.8744 (p90) cc_final: 0.8184 (p90) REVERT: A 365 ILE cc_start: 0.8429 (pt) cc_final: 0.8043 (tt) REVERT: A 576 MET cc_start: 0.8909 (tpt) cc_final: 0.8622 (tpp) REVERT: A 610 MET cc_start: 0.9386 (mmt) cc_final: 0.8938 (mmm) REVERT: A 650 MET cc_start: 0.7424 (ppp) cc_final: 0.7185 (ppp) REVERT: A 797 LYS cc_start: 0.8087 (tttt) cc_final: 0.7837 (tttm) REVERT: A 998 MET cc_start: 0.3878 (ttm) cc_final: 0.3564 (ttm) REVERT: B 398 MET cc_start: 0.3458 (mmt) cc_final: 0.3103 (mmm) REVERT: B 719 TYR cc_start: 0.8416 (m-10) cc_final: 0.7935 (m-10) REVERT: B 825 MET cc_start: 0.7967 (ptt) cc_final: 0.7546 (ptt) REVERT: B 835 TYR cc_start: 0.8419 (m-80) cc_final: 0.8133 (m-10) REVERT: C 178 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6954 (mp10) REVERT: C 206 ASP cc_start: 0.8369 (m-30) cc_final: 0.8146 (p0) REVERT: C 244 ASP cc_start: 0.7917 (m-30) cc_final: 0.7519 (t0) REVERT: C 256 MET cc_start: 0.7894 (pmm) cc_final: 0.7574 (pmm) REVERT: C 462 GLU cc_start: 0.8987 (tp30) cc_final: 0.8705 (tp30) REVERT: C 570 LYS cc_start: 0.9294 (ttmm) cc_final: 0.8905 (tptt) REVERT: C 971 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6079 (tt0) REVERT: C 997 LYS cc_start: 0.8104 (mppt) cc_final: 0.7555 (tptp) REVERT: D 216 LEU cc_start: 0.9055 (tp) cc_final: 0.8799 (tp) REVERT: D 317 MET cc_start: 0.7470 (mmm) cc_final: 0.7223 (tpp) REVERT: D 554 LEU cc_start: 0.9429 (tp) cc_final: 0.9225 (tp) REVERT: D 622 MET cc_start: 0.9200 (ppp) cc_final: 0.8519 (ppp) REVERT: E 376 ASP cc_start: 0.8583 (m-30) cc_final: 0.7945 (p0) REVERT: E 750 MET cc_start: 0.8648 (tpt) cc_final: 0.8412 (tpt) REVERT: E 805 TYR cc_start: 0.7769 (t80) cc_final: 0.7409 (m-80) REVERT: E 944 TYR cc_start: 0.6720 (m-80) cc_final: 0.6029 (m-80) REVERT: E 961 MET cc_start: 0.8969 (mtp) cc_final: 0.7905 (tmm) REVERT: F 278 PHE cc_start: 0.7542 (m-80) cc_final: 0.7021 (m-80) REVERT: F 317 MET cc_start: 0.5038 (tpp) cc_final: 0.3699 (mmt) REVERT: F 335 PHE cc_start: 0.5586 (p90) cc_final: 0.5263 (p90) REVERT: F 443 MET cc_start: 0.8788 (mmt) cc_final: 0.8341 (mmt) REVERT: F 508 MET cc_start: 0.8889 (tpt) cc_final: 0.8660 (tpp) REVERT: F 795 PHE cc_start: 0.8257 (t80) cc_final: 0.7732 (t80) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.5525 time to fit residues: 286.4398 Evaluate side-chains 217 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 180 optimal weight: 0.5980 chunk 483 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 536 optimal weight: 5.9990 chunk 445 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 177 optimal weight: 30.0000 chunk 281 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN B 284 GLN B 824 GLN C 369 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 HIS ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 914 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43921 Z= 0.215 Angle : 0.695 11.436 59408 Z= 0.359 Chirality : 0.046 0.267 6608 Planarity : 0.005 0.061 7665 Dihedral : 11.125 133.747 6286 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.24 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.11), residues: 5543 helix: -0.79 (0.12), residues: 1704 sheet: -1.22 (0.19), residues: 685 loop : -1.79 (0.11), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 715 HIS 0.007 0.001 HIS D 808 PHE 0.038 0.002 PHE E 583 TYR 0.022 0.002 TYR C 13 ARG 0.007 0.001 ARG D1013 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 5.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9207 (mt0) cc_final: 0.8924 (tm-30) REVERT: A 135 MET cc_start: 0.8204 (mmm) cc_final: 0.7961 (mmm) REVERT: A 158 PHE cc_start: 0.8880 (m-10) cc_final: 0.8529 (m-80) REVERT: A 173 VAL cc_start: 0.5880 (t) cc_final: 0.5567 (m) REVERT: A 576 MET cc_start: 0.8688 (tpt) cc_final: 0.8398 (tpp) REVERT: A 610 MET cc_start: 0.9311 (mmt) cc_final: 0.9026 (mmm) REVERT: A 781 MET cc_start: 0.9152 (ppp) cc_final: 0.8682 (ppp) REVERT: A 797 LYS cc_start: 0.7966 (tttt) cc_final: 0.7710 (tttm) REVERT: A 829 PHE cc_start: 0.7385 (t80) cc_final: 0.6986 (t80) REVERT: B 297 TRP cc_start: 0.7575 (m100) cc_final: 0.7353 (m100) REVERT: B 719 TYR cc_start: 0.8120 (m-10) cc_final: 0.7710 (m-10) REVERT: B 816 ARG cc_start: 0.8390 (mmp80) cc_final: 0.8007 (ptp90) REVERT: B 825 MET cc_start: 0.7906 (ptt) cc_final: 0.7316 (ttp) REVERT: B 835 TYR cc_start: 0.8434 (m-80) cc_final: 0.8117 (m-10) REVERT: C 178 GLN cc_start: 0.7275 (tp-100) cc_final: 0.6912 (mp10) REVERT: C 244 ASP cc_start: 0.7835 (m-30) cc_final: 0.7398 (t0) REVERT: C 321 LEU cc_start: 0.8050 (tp) cc_final: 0.7801 (tp) REVERT: C 457 LEU cc_start: 0.9511 (tt) cc_final: 0.9184 (mm) REVERT: C 570 LYS cc_start: 0.9232 (ttmm) cc_final: 0.8789 (tptt) REVERT: C 829 PHE cc_start: 0.8710 (t80) cc_final: 0.8330 (t80) REVERT: C 850 MET cc_start: 0.8889 (ptm) cc_final: 0.8297 (pmm) REVERT: C 971 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5959 (tt0) REVERT: D 216 LEU cc_start: 0.9038 (tp) cc_final: 0.8754 (tp) REVERT: D 317 MET cc_start: 0.7486 (mmm) cc_final: 0.7237 (tpp) REVERT: D 504 GLN cc_start: 0.9296 (mt0) cc_final: 0.9073 (tt0) REVERT: D 622 MET cc_start: 0.9204 (ppp) cc_final: 0.8431 (ppp) REVERT: E 376 ASP cc_start: 0.8555 (m-30) cc_final: 0.7943 (p0) REVERT: E 463 THR cc_start: 0.9379 (t) cc_final: 0.9168 (p) REVERT: E 805 TYR cc_start: 0.7732 (t80) cc_final: 0.7344 (m-80) REVERT: E 851 ASP cc_start: 0.9120 (p0) cc_final: 0.8398 (t70) REVERT: E 944 TYR cc_start: 0.6616 (m-80) cc_final: 0.5958 (m-80) REVERT: E 961 MET cc_start: 0.8931 (mtp) cc_final: 0.7922 (tmm) REVERT: F 278 PHE cc_start: 0.7254 (m-80) cc_final: 0.6976 (m-80) REVERT: F 290 ILE cc_start: 0.9062 (mt) cc_final: 0.8802 (mm) REVERT: F 317 MET cc_start: 0.5114 (tpp) cc_final: 0.3526 (mmt) REVERT: F 622 MET cc_start: 0.7956 (ppp) cc_final: 0.7664 (ppp) REVERT: F 794 LEU cc_start: 0.8742 (mt) cc_final: 0.8491 (mt) REVERT: F 795 PHE cc_start: 0.7727 (t80) cc_final: 0.7355 (t80) REVERT: F 1016 TYR cc_start: 0.6774 (m-80) cc_final: 0.4972 (m-80) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.5240 time to fit residues: 308.1342 Evaluate side-chains 237 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 4.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 517 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 305 optimal weight: 0.9980 chunk 392 optimal weight: 1.9990 chunk 303 optimal weight: 0.0870 chunk 452 optimal weight: 20.0000 chunk 299 optimal weight: 30.0000 chunk 534 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 326 optimal weight: 0.5980 chunk 246 optimal weight: 0.0050 overall best weight: 0.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN B 284 GLN C 154 ASN C 481 HIS C 503 HIS ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 HIS ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 43921 Z= 0.162 Angle : 0.653 10.135 59408 Z= 0.331 Chirality : 0.044 0.215 6608 Planarity : 0.004 0.053 7665 Dihedral : 10.558 131.997 6286 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.35 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.11), residues: 5543 helix: -0.43 (0.12), residues: 1723 sheet: -1.09 (0.19), residues: 712 loop : -1.62 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 547 HIS 0.008 0.001 HIS F 495 PHE 0.029 0.001 PHE E 794 TYR 0.031 0.001 TYR E 128 ARG 0.014 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 4.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5941 (tpt) cc_final: 0.4979 (ptt) REVERT: A 108 GLN cc_start: 0.9188 (mt0) cc_final: 0.8871 (tm-30) REVERT: A 135 MET cc_start: 0.8108 (mmm) cc_final: 0.7880 (mmm) REVERT: A 158 PHE cc_start: 0.8818 (m-10) cc_final: 0.8356 (m-80) REVERT: A 387 LEU cc_start: 0.9042 (tt) cc_final: 0.8840 (tt) REVERT: A 576 MET cc_start: 0.8402 (tpt) cc_final: 0.8172 (tpp) REVERT: A 591 THR cc_start: 0.8249 (p) cc_final: 0.7980 (p) REVERT: A 610 MET cc_start: 0.9226 (mmt) cc_final: 0.8883 (mmm) REVERT: A 781 MET cc_start: 0.9164 (ppp) cc_final: 0.8692 (ppp) REVERT: A 829 PHE cc_start: 0.7626 (t80) cc_final: 0.7280 (t80) REVERT: B 297 TRP cc_start: 0.7425 (m100) cc_final: 0.7168 (m100) REVERT: B 719 TYR cc_start: 0.8092 (m-10) cc_final: 0.7707 (m-10) REVERT: B 816 ARG cc_start: 0.8267 (mmp80) cc_final: 0.7972 (ptp90) REVERT: B 825 MET cc_start: 0.7926 (ptt) cc_final: 0.7306 (ttp) REVERT: B 835 TYR cc_start: 0.8469 (m-80) cc_final: 0.8164 (m-10) REVERT: C 178 GLN cc_start: 0.7188 (tp-100) cc_final: 0.6844 (mp10) REVERT: C 244 ASP cc_start: 0.7745 (m-30) cc_final: 0.7358 (t0) REVERT: C 256 MET cc_start: 0.7670 (pmm) cc_final: 0.7455 (pmm) REVERT: C 321 LEU cc_start: 0.7939 (tp) cc_final: 0.7731 (tp) REVERT: C 457 LEU cc_start: 0.9524 (tt) cc_final: 0.9277 (mm) REVERT: C 570 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8750 (tptt) REVERT: C 829 PHE cc_start: 0.8670 (t80) cc_final: 0.8282 (t80) REVERT: C 850 MET cc_start: 0.8825 (ptm) cc_final: 0.8265 (pmm) REVERT: C 971 GLU cc_start: 0.6487 (mt-10) cc_final: 0.5846 (tt0) REVERT: D 216 LEU cc_start: 0.8950 (tp) cc_final: 0.8674 (tp) REVERT: D 317 MET cc_start: 0.7476 (mmm) cc_final: 0.7212 (tpp) REVERT: D 347 TYR cc_start: 0.6807 (m-10) cc_final: 0.6565 (m-10) REVERT: D 509 GLU cc_start: 0.8769 (tt0) cc_final: 0.8439 (tp30) REVERT: D 514 CYS cc_start: 0.9160 (m) cc_final: 0.8624 (p) REVERT: D 622 MET cc_start: 0.9166 (ppp) cc_final: 0.8103 (ppp) REVERT: D 684 ARG cc_start: 0.7577 (mpp80) cc_final: 0.7175 (ttm170) REVERT: D 711 GLU cc_start: 0.8932 (tt0) cc_final: 0.8601 (tp30) REVERT: D 899 LYS cc_start: 0.5031 (tptt) cc_final: 0.4549 (mmmt) REVERT: E 376 ASP cc_start: 0.8467 (m-30) cc_final: 0.7841 (p0) REVERT: E 511 SER cc_start: 0.8767 (m) cc_final: 0.8282 (t) REVERT: E 805 TYR cc_start: 0.7703 (t80) cc_final: 0.7310 (m-80) REVERT: E 851 ASP cc_start: 0.9105 (p0) cc_final: 0.8412 (t70) REVERT: E 944 TYR cc_start: 0.6684 (m-80) cc_final: 0.6171 (m-80) REVERT: E 961 MET cc_start: 0.8890 (mtp) cc_final: 0.7877 (tmm) REVERT: F 255 LEU cc_start: 0.8740 (tp) cc_final: 0.8301 (pp) REVERT: F 278 PHE cc_start: 0.7223 (m-80) cc_final: 0.6839 (m-80) REVERT: F 317 MET cc_start: 0.5084 (tpp) cc_final: 0.3226 (mmt) REVERT: F 457 ILE cc_start: 0.9490 (mp) cc_final: 0.9242 (mm) REVERT: F 622 MET cc_start: 0.7876 (ppp) cc_final: 0.7646 (ppp) REVERT: F 795 PHE cc_start: 0.7757 (t80) cc_final: 0.7422 (t80) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.4972 time to fit residues: 311.3626 Evaluate side-chains 241 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 330 optimal weight: 4.9990 chunk 213 optimal weight: 0.0070 chunk 319 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 103 optimal weight: 40.0000 chunk 340 optimal weight: 7.9990 chunk 364 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN C 369 ASN C 481 HIS C1005 GLN E 635 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43921 Z= 0.201 Angle : 0.646 10.354 59408 Z= 0.329 Chirality : 0.044 0.209 6608 Planarity : 0.004 0.059 7665 Dihedral : 10.378 129.158 6286 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.55 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 5543 helix: -0.28 (0.12), residues: 1703 sheet: -1.09 (0.19), residues: 709 loop : -1.58 (0.11), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 393 HIS 0.008 0.001 HIS A 406 PHE 0.025 0.002 PHE E 893 TYR 0.020 0.001 TYR E 128 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9185 (mt0) cc_final: 0.8883 (tm-30) REVERT: A 135 MET cc_start: 0.8162 (mmm) cc_final: 0.7919 (mmm) REVERT: A 158 PHE cc_start: 0.8831 (m-10) cc_final: 0.8327 (m-80) REVERT: A 387 LEU cc_start: 0.9042 (tt) cc_final: 0.8819 (tt) REVERT: A 576 MET cc_start: 0.8394 (tpt) cc_final: 0.8116 (tpp) REVERT: A 610 MET cc_start: 0.9226 (mmt) cc_final: 0.8639 (mmm) REVERT: A 781 MET cc_start: 0.9166 (ppp) cc_final: 0.8680 (ppp) REVERT: A 797 LYS cc_start: 0.7950 (tttt) cc_final: 0.7576 (tttm) REVERT: A 829 PHE cc_start: 0.7635 (t80) cc_final: 0.7325 (t80) REVERT: B 297 TRP cc_start: 0.7611 (m100) cc_final: 0.7350 (m100) REVERT: B 719 TYR cc_start: 0.8142 (m-10) cc_final: 0.7783 (m-10) REVERT: B 816 ARG cc_start: 0.8240 (mmp80) cc_final: 0.8035 (ptp90) REVERT: B 825 MET cc_start: 0.7968 (ptt) cc_final: 0.7316 (ttp) REVERT: B 835 TYR cc_start: 0.8503 (m-80) cc_final: 0.8162 (m-10) REVERT: C 178 GLN cc_start: 0.7229 (tp-100) cc_final: 0.6867 (mp10) REVERT: C 244 ASP cc_start: 0.7759 (m-30) cc_final: 0.7384 (t0) REVERT: C 256 MET cc_start: 0.7603 (pmm) cc_final: 0.7381 (pmm) REVERT: C 321 LEU cc_start: 0.7948 (tp) cc_final: 0.7740 (tp) REVERT: C 337 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8528 (ptpt) REVERT: C 457 LEU cc_start: 0.9534 (tt) cc_final: 0.9300 (mm) REVERT: C 560 ASN cc_start: 0.7983 (t0) cc_final: 0.7533 (p0) REVERT: C 570 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8746 (tptt) REVERT: C 669 ASP cc_start: 0.7789 (m-30) cc_final: 0.7483 (m-30) REVERT: C 829 PHE cc_start: 0.8671 (t80) cc_final: 0.8306 (t80) REVERT: C 850 MET cc_start: 0.8839 (ptm) cc_final: 0.8252 (pmm) REVERT: C 971 GLU cc_start: 0.6490 (mt-10) cc_final: 0.5868 (tt0) REVERT: D 216 LEU cc_start: 0.8976 (tp) cc_final: 0.8692 (tp) REVERT: D 317 MET cc_start: 0.7520 (mmm) cc_final: 0.7257 (tpp) REVERT: D 356 LEU cc_start: 0.7768 (pt) cc_final: 0.7498 (pt) REVERT: D 622 MET cc_start: 0.9177 (ppp) cc_final: 0.8456 (ppp) REVERT: D 711 GLU cc_start: 0.8757 (tt0) cc_final: 0.8462 (tp30) REVERT: D 844 ASP cc_start: 0.7822 (p0) cc_final: 0.7572 (p0) REVERT: D 882 ASP cc_start: 0.7207 (m-30) cc_final: 0.6445 (t0) REVERT: D 899 LYS cc_start: 0.4865 (tptt) cc_final: 0.4511 (mmmt) REVERT: E 120 MET cc_start: 0.7859 (tpt) cc_final: 0.7255 (tpp) REVERT: E 376 ASP cc_start: 0.8491 (m-30) cc_final: 0.7863 (p0) REVERT: E 805 TYR cc_start: 0.7730 (t80) cc_final: 0.7291 (m-80) REVERT: E 851 ASP cc_start: 0.9116 (p0) cc_final: 0.8420 (t70) REVERT: E 944 TYR cc_start: 0.6777 (m-80) cc_final: 0.6274 (m-80) REVERT: E 951 MET cc_start: 0.7793 (tmm) cc_final: 0.7579 (tmm) REVERT: E 961 MET cc_start: 0.8869 (mtp) cc_final: 0.7851 (tmm) REVERT: F 278 PHE cc_start: 0.7206 (m-80) cc_final: 0.6818 (m-80) REVERT: F 317 MET cc_start: 0.5065 (tpp) cc_final: 0.3163 (mmt) REVERT: F 443 MET cc_start: 0.8924 (mmt) cc_final: 0.8479 (mmp) REVERT: F 457 ILE cc_start: 0.9489 (mp) cc_final: 0.9213 (mm) REVERT: F 622 MET cc_start: 0.7886 (ppp) cc_final: 0.7642 (ppp) REVERT: F 795 PHE cc_start: 0.7889 (t80) cc_final: 0.7385 (t80) REVERT: F 1016 TYR cc_start: 0.7162 (m-80) cc_final: 0.6029 (m-80) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5185 time to fit residues: 300.8853 Evaluate side-chains 240 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 486 optimal weight: 20.0000 chunk 512 optimal weight: 2.9990 chunk 467 optimal weight: 30.0000 chunk 498 optimal weight: 5.9990 chunk 300 optimal weight: 40.0000 chunk 217 optimal weight: 3.9990 chunk 391 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 471 optimal weight: 30.0000 chunk 496 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43921 Z= 0.265 Angle : 0.687 10.030 59408 Z= 0.353 Chirality : 0.045 0.199 6608 Planarity : 0.005 0.086 7665 Dihedral : 10.486 129.448 6286 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.53 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.11), residues: 5543 helix: -0.43 (0.12), residues: 1697 sheet: -1.15 (0.19), residues: 695 loop : -1.69 (0.11), residues: 3151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 715 HIS 0.009 0.001 HIS C 503 PHE 0.036 0.002 PHE E 583 TYR 0.028 0.002 TYR A 631 ARG 0.006 0.001 ARG D1013 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 5.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9212 (mt0) cc_final: 0.8897 (tm-30) REVERT: A 135 MET cc_start: 0.8289 (mmm) cc_final: 0.8021 (mmm) REVERT: A 158 PHE cc_start: 0.8964 (m-10) cc_final: 0.8440 (m-80) REVERT: A 173 VAL cc_start: 0.5941 (t) cc_final: 0.5682 (m) REVERT: A 387 LEU cc_start: 0.9012 (tt) cc_final: 0.8776 (tt) REVERT: A 576 MET cc_start: 0.8519 (tpt) cc_final: 0.8274 (tpp) REVERT: A 610 MET cc_start: 0.9312 (mmt) cc_final: 0.8719 (mmm) REVERT: A 632 LEU cc_start: 0.9348 (mt) cc_final: 0.8872 (tp) REVERT: A 781 MET cc_start: 0.9168 (ppp) cc_final: 0.8695 (ppp) REVERT: A 797 LYS cc_start: 0.7904 (tttt) cc_final: 0.7624 (tttm) REVERT: A 829 PHE cc_start: 0.7698 (t80) cc_final: 0.7402 (t80) REVERT: A 850 MET cc_start: 0.8532 (tpt) cc_final: 0.8323 (tmm) REVERT: B 297 TRP cc_start: 0.7752 (m100) cc_final: 0.7437 (m100) REVERT: B 508 MET cc_start: 0.8831 (ptt) cc_final: 0.8609 (ptt) REVERT: B 719 TYR cc_start: 0.8212 (m-10) cc_final: 0.7823 (m-10) REVERT: B 816 ARG cc_start: 0.8296 (mmp80) cc_final: 0.8018 (ptp90) REVERT: B 825 MET cc_start: 0.7997 (ptt) cc_final: 0.7370 (ttp) REVERT: B 835 TYR cc_start: 0.8509 (m-80) cc_final: 0.8188 (m-10) REVERT: C 178 GLN cc_start: 0.7248 (tp-100) cc_final: 0.6873 (mm-40) REVERT: C 244 ASP cc_start: 0.7774 (m-30) cc_final: 0.7412 (t0) REVERT: C 321 LEU cc_start: 0.7988 (tp) cc_final: 0.7763 (tp) REVERT: C 457 LEU cc_start: 0.9538 (tt) cc_final: 0.9280 (mm) REVERT: C 570 LYS cc_start: 0.9240 (ttmm) cc_final: 0.8791 (tptt) REVERT: C 829 PHE cc_start: 0.8666 (t80) cc_final: 0.8285 (t80) REVERT: C 850 MET cc_start: 0.8907 (ptm) cc_final: 0.8261 (pmm) REVERT: D 216 LEU cc_start: 0.8954 (tp) cc_final: 0.8666 (tp) REVERT: D 317 MET cc_start: 0.7553 (mmm) cc_final: 0.7299 (tpp) REVERT: D 509 GLU cc_start: 0.9132 (tt0) cc_final: 0.8895 (tt0) REVERT: D 622 MET cc_start: 0.9240 (ppp) cc_final: 0.8641 (ppp) REVERT: D 844 ASP cc_start: 0.7807 (p0) cc_final: 0.7514 (p0) REVERT: D 882 ASP cc_start: 0.7276 (m-30) cc_final: 0.6522 (t0) REVERT: D 899 LYS cc_start: 0.4835 (tptt) cc_final: 0.4567 (mmmt) REVERT: E 120 MET cc_start: 0.7852 (tpt) cc_final: 0.7282 (tpp) REVERT: E 376 ASP cc_start: 0.8498 (m-30) cc_final: 0.7883 (p0) REVERT: E 805 TYR cc_start: 0.7734 (t80) cc_final: 0.7305 (m-80) REVERT: E 944 TYR cc_start: 0.6797 (m-80) cc_final: 0.6262 (m-80) REVERT: E 951 MET cc_start: 0.7818 (tmm) cc_final: 0.7268 (ttp) REVERT: E 961 MET cc_start: 0.8891 (mtp) cc_final: 0.7875 (tmm) REVERT: F 278 PHE cc_start: 0.7248 (m-80) cc_final: 0.6836 (m-80) REVERT: F 317 MET cc_start: 0.5179 (tpp) cc_final: 0.3270 (mmt) REVERT: F 622 MET cc_start: 0.7948 (ppp) cc_final: 0.7690 (ppp) REVERT: F 794 LEU cc_start: 0.8747 (mt) cc_final: 0.8498 (mt) REVERT: F 795 PHE cc_start: 0.7993 (t80) cc_final: 0.7431 (t80) REVERT: F 1016 TYR cc_start: 0.7177 (m-80) cc_final: 0.5914 (m-80) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5063 time to fit residues: 268.9638 Evaluate side-chains 232 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 327 optimal weight: 1.9990 chunk 527 optimal weight: 20.0000 chunk 321 optimal weight: 0.9990 chunk 250 optimal weight: 20.0000 chunk 366 optimal weight: 50.0000 chunk 552 optimal weight: 9.9990 chunk 508 optimal weight: 7.9990 chunk 440 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 340 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN C1005 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 HIS ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43921 Z= 0.225 Angle : 0.664 11.044 59408 Z= 0.338 Chirality : 0.044 0.203 6608 Planarity : 0.004 0.075 7665 Dihedral : 10.378 133.918 6286 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.42 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.11), residues: 5543 helix: -0.36 (0.12), residues: 1694 sheet: -1.23 (0.19), residues: 723 loop : -1.71 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 715 HIS 0.013 0.001 HIS F 495 PHE 0.024 0.002 PHE E 893 TYR 0.025 0.002 TYR B 737 ARG 0.006 0.001 ARG D1013 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9224 (mt0) cc_final: 0.8898 (tm-30) REVERT: A 135 MET cc_start: 0.8340 (mmm) cc_final: 0.8059 (mmm) REVERT: A 158 PHE cc_start: 0.8948 (m-10) cc_final: 0.8427 (m-80) REVERT: A 387 LEU cc_start: 0.8945 (tt) cc_final: 0.8703 (tt) REVERT: A 610 MET cc_start: 0.9276 (mmt) cc_final: 0.8700 (mmm) REVERT: A 632 LEU cc_start: 0.9321 (mt) cc_final: 0.8858 (tp) REVERT: A 781 MET cc_start: 0.9101 (ppp) cc_final: 0.8645 (ppp) REVERT: A 797 LYS cc_start: 0.7861 (tttt) cc_final: 0.7579 (tttm) REVERT: A 829 PHE cc_start: 0.7660 (t80) cc_final: 0.7385 (t80) REVERT: A 850 MET cc_start: 0.8444 (tpt) cc_final: 0.8242 (tmm) REVERT: B 297 TRP cc_start: 0.7653 (m100) cc_final: 0.7332 (m100) REVERT: B 719 TYR cc_start: 0.8119 (m-10) cc_final: 0.7758 (m-10) REVERT: B 816 ARG cc_start: 0.8267 (mmp80) cc_final: 0.8027 (ptp90) REVERT: B 825 MET cc_start: 0.7907 (ptt) cc_final: 0.7411 (ttp) REVERT: B 835 TYR cc_start: 0.8491 (m-80) cc_final: 0.8158 (m-10) REVERT: C 178 GLN cc_start: 0.7108 (tp-100) cc_final: 0.6767 (mm-40) REVERT: C 244 ASP cc_start: 0.7764 (m-30) cc_final: 0.7409 (t0) REVERT: C 321 LEU cc_start: 0.7914 (tp) cc_final: 0.7658 (tp) REVERT: C 457 LEU cc_start: 0.9545 (tt) cc_final: 0.9276 (mm) REVERT: C 560 ASN cc_start: 0.7854 (t0) cc_final: 0.7304 (p0) REVERT: C 570 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8796 (tptt) REVERT: C 669 ASP cc_start: 0.7703 (m-30) cc_final: 0.7406 (m-30) REVERT: C 829 PHE cc_start: 0.8645 (t80) cc_final: 0.8280 (t80) REVERT: C 850 MET cc_start: 0.8889 (ptm) cc_final: 0.8262 (pmm) REVERT: C 955 MET cc_start: 0.8508 (mpp) cc_final: 0.7525 (mpp) REVERT: D 216 LEU cc_start: 0.8963 (tp) cc_final: 0.8672 (tp) REVERT: D 317 MET cc_start: 0.7557 (mmm) cc_final: 0.7298 (tpp) REVERT: D 514 CYS cc_start: 0.9185 (m) cc_final: 0.8695 (p) REVERT: D 622 MET cc_start: 0.9181 (ppp) cc_final: 0.8577 (ppp) REVERT: D 844 ASP cc_start: 0.7806 (p0) cc_final: 0.7481 (p0) REVERT: D 882 ASP cc_start: 0.7303 (m-30) cc_final: 0.6603 (t0) REVERT: D 899 LYS cc_start: 0.4734 (tptt) cc_final: 0.4467 (mmmt) REVERT: E 120 MET cc_start: 0.7816 (tpt) cc_final: 0.7511 (tpt) REVERT: E 376 ASP cc_start: 0.8529 (m-30) cc_final: 0.7940 (p0) REVERT: E 762 MET cc_start: 0.3096 (tpt) cc_final: 0.2751 (tpt) REVERT: E 805 TYR cc_start: 0.7656 (t80) cc_final: 0.7268 (m-80) REVERT: E 944 TYR cc_start: 0.6814 (m-80) cc_final: 0.6290 (m-80) REVERT: E 951 MET cc_start: 0.7789 (tmm) cc_final: 0.7294 (ttp) REVERT: E 961 MET cc_start: 0.8866 (mtp) cc_final: 0.7861 (tmm) REVERT: F 278 PHE cc_start: 0.7196 (m-80) cc_final: 0.6788 (m-80) REVERT: F 443 MET cc_start: 0.8894 (mmt) cc_final: 0.8357 (mmp) REVERT: F 457 ILE cc_start: 0.9516 (mp) cc_final: 0.9267 (mm) REVERT: F 795 PHE cc_start: 0.7864 (t80) cc_final: 0.7366 (t80) REVERT: F 1016 TYR cc_start: 0.7143 (m-80) cc_final: 0.6011 (m-80) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.5629 time to fit residues: 309.8324 Evaluate side-chains 236 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 349 optimal weight: 1.9990 chunk 469 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 405 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 440 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 452 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 967 GLN C1005 GLN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.076535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058936 restraints weight = 257828.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058262 restraints weight = 182372.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058442 restraints weight = 145521.051| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43921 Z= 0.174 Angle : 0.638 10.056 59408 Z= 0.321 Chirality : 0.044 0.213 6608 Planarity : 0.004 0.067 7665 Dihedral : 10.151 134.653 6286 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.50 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.11), residues: 5543 helix: -0.29 (0.12), residues: 1716 sheet: -1.13 (0.19), residues: 714 loop : -1.68 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 598 HIS 0.005 0.001 HIS D 808 PHE 0.036 0.001 PHE E 583 TYR 0.019 0.001 TYR B 737 ARG 0.006 0.000 ARG D1013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8856.57 seconds wall clock time: 163 minutes 44.82 seconds (9824.82 seconds total)