Starting phenix.real_space_refine on Sun Aug 24 19:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7w_38129/08_2025/8x7w_38129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7w_38129/08_2025/8x7w_38129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x7w_38129/08_2025/8x7w_38129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7w_38129/08_2025/8x7w_38129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x7w_38129/08_2025/8x7w_38129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7w_38129/08_2025/8x7w_38129.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 14235 2.51 5 N 3921 2.21 5 O 4057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22389 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7662 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 36, 'TRANS': 939} Chain breaks: 6 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 780 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "C" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2756 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 332} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7662 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 36, 'TRANS': 939} Chain breaks: 6 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 773 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "F" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2756 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 332} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.29, per 1000 atoms: 0.19 Number of scatterers: 22389 At special positions: 0 Unit cell: (99, 119.9, 222.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 4057 8.00 N 3921 7.00 C 14235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5346 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 27 sheets defined 45.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.679A pdb=" N GLY A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 136 through 150 Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.584A pdb=" N LYS A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.537A pdb=" N TRP A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 521 through 541 Processing helix chain 'A' and resid 547 through 555 Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.382A pdb=" N LYS A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 642 through 654 Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.626A pdb=" N LYS A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.558A pdb=" N ASN A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 728 removed outlier: 3.519A pdb=" N LEU A 727 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 Processing helix chain 'A' and resid 764 through 780 Processing helix chain 'A' and resid 794 through 804 removed outlier: 3.522A pdb=" N LYS A 804 " --> pdb=" O THR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 4.900A pdb=" N GLN A 827 " --> pdb=" O PRO A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 removed outlier: 4.398A pdb=" N ILE A 832 " --> pdb=" O HIS A 828 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 Processing helix chain 'A' and resid 879 through 893 Processing helix chain 'A' and resid 907 through 920 Proline residue: A 913 - end of helix removed outlier: 3.848A pdb=" N VAL A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 963 through 976 removed outlier: 4.091A pdb=" N GLY A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 Processing helix chain 'A' and resid 1021 through 1033 removed outlier: 3.616A pdb=" N VAL A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1064 removed outlier: 3.613A pdb=" N CYS A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1090 Processing helix chain 'A' and resid 1107 through 1121 Processing helix chain 'A' and resid 1135 through 1148 removed outlier: 3.629A pdb=" N CYS A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1177 Processing helix chain 'A' and resid 1192 through 1200 removed outlier: 4.544A pdb=" N TYR A1196 " --> pdb=" O GLU A1192 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A1199 " --> pdb=" O ARG A1195 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.662A pdb=" N GLU B 45 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 47 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 99 through 124 Processing helix chain 'C' and resid 154 through 169 removed outlier: 4.118A pdb=" N THR C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.703A pdb=" N GLU D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 97 through 104 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 133 Processing helix chain 'D' and resid 136 through 150 Processing helix chain 'D' and resid 231 through 250 Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 321 through 327 removed outlier: 3.908A pdb=" N LYS D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 340 Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 363 through 366 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.966A pdb=" N LEU D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 397 Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 497 through 511 removed outlier: 3.567A pdb=" N LEU D 501 " --> pdb=" O THR D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 Processing helix chain 'D' and resid 547 through 555 Processing helix chain 'D' and resid 557 through 565 Processing helix chain 'D' and resid 585 through 598 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.803A pdb=" N LYS D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 4.401A pdb=" N MET D 633 " --> pdb=" O HIS D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 654 Proline residue: D 648 - end of helix Processing helix chain 'D' and resid 660 through 674 Processing helix chain 'D' and resid 680 through 695 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 716 through 728 removed outlier: 3.689A pdb=" N GLN D 728 " --> pdb=" O SER D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 762 Processing helix chain 'D' and resid 764 through 780 Processing helix chain 'D' and resid 794 through 806 Processing helix chain 'D' and resid 822 through 824 No H-bonds generated for 'chain 'D' and resid 822 through 824' Processing helix chain 'D' and resid 825 through 836 removed outlier: 3.806A pdb=" N TRP D 830 " --> pdb=" O VAL D 826 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG D 831 " --> pdb=" O GLN D 827 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D 832 " --> pdb=" O HIS D 828 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL D 833 " --> pdb=" O LEU D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 862 Processing helix chain 'D' and resid 879 through 893 Processing helix chain 'D' and resid 907 through 910 Processing helix chain 'D' and resid 911 through 920 removed outlier: 3.647A pdb=" N VAL D 920 " --> pdb=" O ASP D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 950 Processing helix chain 'D' and resid 963 through 976 removed outlier: 3.563A pdb=" N GLY D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1005 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1050 through 1064 removed outlier: 3.519A pdb=" N CYS D1054 " --> pdb=" O THR D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1090 removed outlier: 3.641A pdb=" N GLY D1081 " --> pdb=" O LEU D1077 " (cutoff:3.500A) Processing helix chain 'D' and resid 1107 through 1121 Processing helix chain 'D' and resid 1135 through 1148 removed outlier: 3.504A pdb=" N CYS D1148 " --> pdb=" O SER D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1159 through 1163 removed outlier: 3.586A pdb=" N GLN D1162 " --> pdb=" O TRP D1159 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR D1163 " --> pdb=" O LYS D1160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1159 through 1163' Processing helix chain 'D' and resid 1164 through 1177 Processing helix chain 'D' and resid 1192 through 1199 removed outlier: 4.305A pdb=" N TYR D1196 " --> pdb=" O GLU D1192 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 69 through 78 Processing helix chain 'E' and resid 99 through 124 Processing helix chain 'F' and resid 154 through 169 removed outlier: 4.028A pdb=" N THR F 158 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU F 159 " --> pdb=" O TRP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.782A pdb=" N THR A 408 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 317 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASP A 362 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU A 319 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 711 removed outlier: 3.654A pdb=" N VAL A 710 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 737 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 736 " --> pdb=" O ASP A 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 873 through 874 removed outlier: 3.847A pdb=" N ALA A 902 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 959 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 985 " --> pdb=" O HIS A1012 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A1014 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A1013 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1072 through 1073 removed outlier: 7.011A pdb=" N LEU A1072 " --> pdb=" O LYS A1102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AA7, first strand: chain 'C' and resid 278 through 284 removed outlier: 6.135A pdb=" N LYS C 279 " --> pdb=" O GLN C 569 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN C 569 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 281 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 557 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS C 547 " --> pdb=" O GLY C 560 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 291 through 294 removed outlier: 3.810A pdb=" N ALA C 291 " --> pdb=" O CYS C 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 342 removed outlier: 3.731A pdb=" N THR C 339 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY C 352 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 359 " --> pdb=" O GLN C 374 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 374 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL C 361 " --> pdb=" O LYS C 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 382 through 388 removed outlier: 6.710A pdb=" N SER C 397 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU C 385 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE C 395 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA C 387 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 393 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 396 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 426 through 430 removed outlier: 3.554A pdb=" N LYS C 430 " --> pdb=" O ASN C 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 466 through 468 removed outlier: 3.594A pdb=" N LEU C 477 " --> pdb=" O TRP C 485 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 485 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN C 484 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 504 through 509 removed outlier: 3.716A pdb=" N GLY C 520 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N PHE C 524 " --> pdb=" O GLY C 520 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 537 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 529 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 535 " --> pdb=" O SER C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 317 through 320 removed outlier: 3.747A pdb=" N ASP D 362 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE D 359 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR D 408 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 361 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 282 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR D 426 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 712 through 713 removed outlier: 3.677A pdb=" N LEU D 712 " --> pdb=" O ARG D 737 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP D 739 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP D 787 " --> pdb=" O ILE D 736 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 738 " --> pdb=" O ASP D 787 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 791 through 792 removed outlier: 6.777A pdb=" N SER D 791 " --> pdb=" O GLN D 821 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 873 through 874 removed outlier: 3.500A pdb=" N ALA D 902 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 959 " --> pdb=" O LEU D 930 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1012 through 1014 removed outlier: 7.617A pdb=" N LEU D1013 " --> pdb=" O GLU D1043 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N VAL D1045 " --> pdb=" O LEU D1013 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR D1073 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU D1044 " --> pdb=" O THR D1073 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU D1072 " --> pdb=" O LYS D1102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 50 through 55 removed outlier: 3.580A pdb=" N LEU E 50 " --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 320 through 321 removed outlier: 8.678A pdb=" N ASP F 321 " --> pdb=" O MET F 280 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 282 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS F 279 " --> pdb=" O GLN F 569 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN F 569 " --> pdb=" O LYS F 279 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 281 " --> pdb=" O VAL F 567 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL F 557 " --> pdb=" O TYR F 568 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS F 547 " --> pdb=" O GLY F 560 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 291 through 294 removed outlier: 4.406A pdb=" N ALA F 291 " --> pdb=" O CYS F 304 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 339 through 342 removed outlier: 3.711A pdb=" N THR F 339 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY F 352 " --> pdb=" O THR F 339 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 341 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F 361 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU F 373 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 382 through 388 removed outlier: 3.729A pdb=" N ALA F 384 " --> pdb=" O SER F 397 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP F 386 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE F 395 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 394 " --> pdb=" O TRP F 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 382 through 388 removed outlier: 3.729A pdb=" N ALA F 384 " --> pdb=" O SER F 397 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP F 386 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE F 395 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 396 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG F 404 " --> pdb=" O ALA F 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 402 " --> pdb=" O PHE F 398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 426 through 430 removed outlier: 3.542A pdb=" N CYS F 445 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 455 " --> pdb=" O CYS F 445 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 466 through 468 Processing sheet with id=AC9, first strand: chain 'F' and resid 504 through 509 removed outlier: 3.744A pdb=" N SER F 506 " --> pdb=" O VAL F 519 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY F 520 " --> pdb=" O PHE F 524 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE F 524 " --> pdb=" O GLY F 520 " (cutoff:3.500A) 999 hydrogen bonds defined for protein. 2880 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: 4.11 Time building geometry restraints manager: 2.46 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: 5928 1.33 - 1.45: 3969 1.45 - 1.57: 12735 1.57 - 1.69: 0 1.69 - 1.81: 246 Bond restraints: 22878 Sorted by residual: bond pdb=" N ARG E 37 " pdb=" CA ARG E 37 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.61e-02 3.86e+03 5.03e+00 bond pdb=" N TRP E 39 " pdb=" CA TRP E 39 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" C PRO F 251 " pdb=" O PRO F 251 " ideal model delta sigma weight residual 1.238 1.213 0.025 1.35e-02 5.49e+03 3.31e+00 bond pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 22873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 30164 1.48 - 2.96: 670 2.96 - 4.44: 140 4.44 - 5.92: 9 5.92 - 7.40: 4 Bond angle restraints: 30987 Sorted by residual: angle pdb=" N VAL F 414 " pdb=" CA VAL F 414 " pdb=" C VAL F 414 " ideal model delta sigma weight residual 111.62 108.58 3.04 7.90e-01 1.60e+00 1.48e+01 angle pdb=" CA MET D 834 " pdb=" CB MET D 834 " pdb=" CG MET D 834 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C ARG E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta sigma weight residual 119.85 123.02 -3.17 1.01e+00 9.80e-01 9.82e+00 angle pdb=" CA PRO D 424 " pdb=" N PRO D 424 " pdb=" CD PRO D 424 " ideal model delta sigma weight residual 112.00 108.03 3.97 1.40e+00 5.10e-01 8.04e+00 angle pdb=" N VAL C 414 " pdb=" CA VAL C 414 " pdb=" C VAL C 414 " ideal model delta sigma weight residual 111.67 109.09 2.58 9.50e-01 1.11e+00 7.35e+00 ... (remaining 30982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 12560 17.77 - 35.54: 933 35.54 - 53.31: 209 53.31 - 71.08: 21 71.08 - 88.85: 9 Dihedral angle restraints: 13732 sinusoidal: 5529 harmonic: 8203 Sorted by residual: dihedral pdb=" CD ARG E 37 " pdb=" NE ARG E 37 " pdb=" CZ ARG E 37 " pdb=" NH1 ARG E 37 " ideal model delta sinusoidal sigma weight residual 0.00 38.43 -38.43 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CA PRO D 424 " pdb=" C PRO D 424 " pdb=" N ARG D 425 " pdb=" CA ARG D 425 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE C 297 " pdb=" C PHE C 297 " pdb=" N THR C 298 " pdb=" CA THR C 298 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 13729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2526 0.033 - 0.067: 668 0.067 - 0.100: 161 0.100 - 0.134: 130 0.134 - 0.167: 6 Chirality restraints: 3491 Sorted by residual: chirality pdb=" CB THR A 241 " pdb=" CA THR A 241 " pdb=" OG1 THR A 241 " pdb=" CG2 THR A 241 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA VAL D1130 " pdb=" N VAL D1130 " pdb=" C VAL D1130 " pdb=" CB VAL D1130 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA VAL A1045 " pdb=" N VAL A1045 " pdb=" C VAL A1045 " pdb=" CB VAL A1045 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 3488 not shown) Planarity restraints: 3929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 37 " 0.673 9.50e-02 1.11e+02 3.02e-01 5.54e+01 pdb=" NE ARG E 37 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG E 37 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 37 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 37 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 423 " -0.084 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO D 424 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 424 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO D 424 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 438 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO C 439 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 439 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 439 " 0.034 5.00e-02 4.00e+02 ... (remaining 3926 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 254 2.60 - 3.17: 19836 3.17 - 3.75: 32837 3.75 - 4.32: 43234 4.32 - 4.90: 73464 Nonbonded interactions: 169625 Sorted by model distance: nonbonded pdb=" OG SER F 510 " pdb=" O TRP F 515 " model vdw 2.022 3.040 nonbonded pdb=" OG SER A 642 " pdb=" OD1 ASP A 644 " model vdw 2.045 3.040 nonbonded pdb=" O MET D 760 " pdb=" OG1 THR D 764 " model vdw 2.060 3.040 nonbonded pdb=" O LEU A1118 " pdb=" OG SER A1151 " model vdw 2.061 3.040 nonbonded pdb=" O ARG A 136 " pdb=" OG SER A 139 " model vdw 2.078 3.040 ... (remaining 169620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 33 through 124) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.810 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22878 Z= 0.141 Angle : 0.558 7.402 30987 Z= 0.311 Chirality : 0.038 0.167 3491 Planarity : 0.006 0.302 3929 Dihedral : 13.057 88.851 8386 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.04 % Allowed : 12.33 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2791 helix: 2.13 (0.15), residues: 1186 sheet: -0.91 (0.24), residues: 473 loop : -1.20 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.019 0.001 TYR A 70 PHE 0.013 0.001 PHE D 99 TRP 0.012 0.001 TRP A1161 HIS 0.006 0.001 HIS D 863 Details of bonding type rmsd covalent geometry : bond 0.00287 (22878) covalent geometry : angle 0.55792 (30987) hydrogen bonds : bond 0.18383 ( 996) hydrogen bonds : angle 6.16910 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.4761 (tmm) cc_final: 0.4151 (ptt) REVERT: A 540 TRP cc_start: 0.6899 (m100) cc_final: 0.6153 (m100) REVERT: A 874 ASP cc_start: 0.6753 (m-30) cc_final: 0.6238 (m-30) REVERT: D 932 ASP cc_start: 0.5622 (t0) cc_final: 0.5393 (t70) REVERT: F 456 GLU cc_start: 0.5474 (tm-30) cc_final: 0.5025 (tp30) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1447 time to fit residues: 53.5334 Evaluate side-chains 208 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 807 HIS A1200 ASN C 433 ASN F 495 HIS F 564 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.226283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.185096 restraints weight = 34435.473| |-----------------------------------------------------------------------------| r_work (start): 0.4499 rms_B_bonded: 2.96 r_work: 0.4105 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22878 Z= 0.128 Angle : 0.587 7.559 30987 Z= 0.299 Chirality : 0.042 0.161 3491 Planarity : 0.004 0.093 3929 Dihedral : 3.912 33.439 3027 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.78 % Allowed : 12.45 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2791 helix: 2.08 (0.15), residues: 1219 sheet: -0.82 (0.23), residues: 527 loop : -0.99 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 855 TYR 0.030 0.001 TYR A 883 PHE 0.015 0.001 PHE D 60 TRP 0.023 0.002 TRP F 406 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00284 (22878) covalent geometry : angle 0.58700 (30987) hydrogen bonds : bond 0.04485 ( 996) hydrogen bonds : angle 4.66899 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.4922 (tmm) cc_final: 0.4471 (ptt) REVERT: A 406 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7693 (mt) REVERT: A 430 ARG cc_start: 0.6828 (tpt90) cc_final: 0.6607 (tpt90) REVERT: A 540 TRP cc_start: 0.6900 (m100) cc_final: 0.6067 (m100) REVERT: A 874 ASP cc_start: 0.6666 (m-30) cc_final: 0.6339 (m-30) REVERT: A 1044 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 37 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7920 (ptt90) REVERT: B 121 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.6727 (ptm160) REVERT: C 161 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7531 (tp30) REVERT: C 254 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5112 (m-80) REVERT: C 463 ILE cc_start: 0.8078 (mp) cc_final: 0.7859 (mp) REVERT: D 87 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6560 (pptt) REVERT: D 932 ASP cc_start: 0.6541 (t0) cc_final: 0.6228 (t70) REVERT: D 1044 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5533 (pp) REVERT: E 81 LEU cc_start: 0.8798 (pp) cc_final: 0.8582 (tt) REVERT: F 254 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.4922 (t80) REVERT: F 456 GLU cc_start: 0.5471 (tm-30) cc_final: 0.4904 (tp30) REVERT: F 509 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5028 (t80) outliers start: 44 outliers final: 13 residues processed: 264 average time/residue: 0.1308 time to fit residues: 54.3387 Evaluate side-chains 227 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 249 optimal weight: 0.2980 chunk 269 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 263 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 241 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS D1012 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.223121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.4386 r_free = 0.4386 target = 0.170744 restraints weight = 34708.966| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.91 r_work: 0.4023 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22878 Z= 0.184 Angle : 0.631 9.129 30987 Z= 0.319 Chirality : 0.043 0.196 3491 Planarity : 0.004 0.050 3929 Dihedral : 4.246 33.015 3027 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.32 % Allowed : 13.06 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.16), residues: 2791 helix: 1.76 (0.15), residues: 1208 sheet: -1.06 (0.23), residues: 521 loop : -1.09 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 646 TYR 0.020 0.002 TYR A 426 PHE 0.017 0.002 PHE A 773 TRP 0.023 0.002 TRP D 340 HIS 0.005 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00430 (22878) covalent geometry : angle 0.63081 (30987) hydrogen bonds : bond 0.04846 ( 996) hydrogen bonds : angle 4.64238 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 223 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.5811 (t80) REVERT: A 324 MET cc_start: 0.6327 (mmm) cc_final: 0.5932 (mpp) REVERT: A 406 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7627 (mt) REVERT: A 430 ARG cc_start: 0.7152 (tpt90) cc_final: 0.6780 (mmm160) REVERT: A 540 TRP cc_start: 0.6931 (m100) cc_final: 0.5939 (m100) REVERT: A 874 ASP cc_start: 0.6838 (m-30) cc_final: 0.6455 (m-30) REVERT: A 1044 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7983 (pp) REVERT: B 37 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8175 (ptt90) REVERT: B 121 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.6692 (ptm160) REVERT: C 161 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: C 463 ILE cc_start: 0.8271 (mp) cc_final: 0.7965 (mp) REVERT: C 542 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6828 (mmm) REVERT: D 280 ARG cc_start: 0.3589 (ttt180) cc_final: 0.3273 (ttt180) REVERT: D 659 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.2059 (pp) REVERT: D 932 ASP cc_start: 0.7091 (t0) cc_final: 0.6862 (t70) REVERT: E 81 LEU cc_start: 0.8896 (pp) cc_final: 0.8630 (tt) REVERT: F 254 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.4737 (t80) REVERT: F 509 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5040 (t80) REVERT: F 514 GLN cc_start: 0.6278 (mm-40) cc_final: 0.5720 (mt0) outliers start: 82 outliers final: 44 residues processed: 283 average time/residue: 0.1407 time to fit residues: 62.2952 Evaluate side-chains 253 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1079 ASP Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1121 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 479 MET Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 235 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 260 optimal weight: 0.0770 chunk 274 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 258 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 GLN A 838 ASN A 880 HIS D 716 GLN D 904 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.224552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.171591 restraints weight = 34793.751| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 4.10 r_work: 0.4039 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22878 Z= 0.140 Angle : 0.586 9.790 30987 Z= 0.291 Chirality : 0.042 0.193 3491 Planarity : 0.004 0.049 3929 Dihedral : 4.153 32.593 3027 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.23 % Allowed : 14.68 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.16), residues: 2791 helix: 1.77 (0.15), residues: 1210 sheet: -0.77 (0.23), residues: 527 loop : -1.18 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 617 TYR 0.019 0.001 TYR A 883 PHE 0.013 0.001 PHE F 254 TRP 0.019 0.001 TRP F 406 HIS 0.004 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00323 (22878) covalent geometry : angle 0.58552 (30987) hydrogen bonds : bond 0.04050 ( 996) hydrogen bonds : angle 4.41240 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 229 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6026 (t80) REVERT: A 240 MET cc_start: 0.4989 (tmm) cc_final: 0.4153 (ptt) REVERT: A 406 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7656 (mt) REVERT: A 540 TRP cc_start: 0.6899 (m100) cc_final: 0.5885 (m100) REVERT: A 794 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.6267 (p) REVERT: A 874 ASP cc_start: 0.6764 (m-30) cc_final: 0.6492 (m-30) REVERT: A 1044 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 1143 CYS cc_start: 0.7790 (m) cc_final: 0.7279 (m) REVERT: B 37 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8277 (ptt90) REVERT: B 121 ARG cc_start: 0.7156 (mmm-85) cc_final: 0.6706 (ptm160) REVERT: C 161 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: C 254 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5082 (m-80) REVERT: C 463 ILE cc_start: 0.8258 (mp) cc_final: 0.7876 (mp) REVERT: C 542 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6956 (mmm) REVERT: D 932 ASP cc_start: 0.6998 (t0) cc_final: 0.6692 (t70) REVERT: E 81 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (tt) REVERT: F 254 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.4622 (t80) REVERT: F 464 MET cc_start: 0.6155 (pmm) cc_final: 0.4921 (pmm) REVERT: F 485 TRP cc_start: 0.5661 (m100) cc_final: 0.5441 (m100) REVERT: F 509 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5093 (t80) REVERT: F 514 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5817 (mt0) outliers start: 80 outliers final: 48 residues processed: 286 average time/residue: 0.1384 time to fit residues: 62.2760 Evaluate side-chains 262 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1079 ASP Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 816 MET Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1121 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 154 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 166 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 HIS E 33 GLN F 245 GLN ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.221344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.170703 restraints weight = 34540.973| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.88 r_work: 0.4009 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22878 Z= 0.191 Angle : 0.651 16.236 30987 Z= 0.325 Chirality : 0.043 0.168 3491 Planarity : 0.004 0.056 3929 Dihedral : 4.430 33.221 3027 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.29 % Allowed : 15.65 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2791 helix: 1.50 (0.15), residues: 1210 sheet: -1.10 (0.22), residues: 537 loop : -1.25 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 430 TYR 0.022 0.002 TYR A 70 PHE 0.017 0.002 PHE A 404 TRP 0.032 0.002 TRP F 406 HIS 0.006 0.001 HIS D1012 Details of bonding type rmsd covalent geometry : bond 0.00448 (22878) covalent geometry : angle 0.65100 (30987) hydrogen bonds : bond 0.04742 ( 996) hydrogen bonds : angle 4.56631 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 212 time to evaluate : 0.860 Fit side-chains REVERT: A 70 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6671 (t80) REVERT: A 305 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: A 324 MET cc_start: 0.6397 (mmm) cc_final: 0.6026 (mpp) REVERT: A 406 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 430 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6750 (mmm160) REVERT: A 794 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6298 (p) REVERT: A 874 ASP cc_start: 0.6734 (m-30) cc_final: 0.6502 (m-30) REVERT: A 1044 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8018 (pp) REVERT: A 1143 CYS cc_start: 0.7780 (m) cc_final: 0.7345 (m) REVERT: B 37 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8394 (ptt90) REVERT: C 161 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: C 254 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: C 303 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6950 (m) REVERT: C 463 ILE cc_start: 0.8331 (mp) cc_final: 0.7954 (mp) REVERT: C 542 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6977 (mmm) REVERT: D 659 LEU cc_start: 0.2269 (OUTLIER) cc_final: 0.1848 (pp) REVERT: D 686 ASP cc_start: 0.7126 (t0) cc_final: 0.6825 (t0) REVERT: D 932 ASP cc_start: 0.6924 (t0) cc_final: 0.6717 (t70) REVERT: F 254 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.4667 (t80) REVERT: F 464 MET cc_start: 0.6448 (pmm) cc_final: 0.5185 (pmm) REVERT: F 485 TRP cc_start: 0.5798 (m100) cc_final: 0.5585 (m100) REVERT: F 509 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5151 (t80) REVERT: F 514 GLN cc_start: 0.6231 (mm-40) cc_final: 0.5772 (mt0) outliers start: 106 outliers final: 70 residues processed: 294 average time/residue: 0.1356 time to fit residues: 63.3183 Evaluate side-chains 288 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 205 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1079 ASP Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1121 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1198 TRP Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 537 PHE Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 159 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 275 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.218785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.168422 restraints weight = 34801.815| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.87 r_work: 0.3977 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22878 Z= 0.246 Angle : 0.720 15.455 30987 Z= 0.364 Chirality : 0.046 0.176 3491 Planarity : 0.005 0.064 3929 Dihedral : 4.862 35.429 3027 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.14 % Allowed : 16.17 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2791 helix: 1.09 (0.15), residues: 1212 sheet: -1.62 (0.21), residues: 553 loop : -1.41 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 121 TYR 0.026 0.002 TYR A 70 PHE 0.022 0.002 PHE A 707 TRP 0.028 0.002 TRP F 406 HIS 0.008 0.002 HIS D1012 Details of bonding type rmsd covalent geometry : bond 0.00578 (22878) covalent geometry : angle 0.71955 (30987) hydrogen bonds : bond 0.05411 ( 996) hydrogen bonds : angle 4.83520 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 220 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6150 (t80) REVERT: A 240 MET cc_start: 0.5224 (tmm) cc_final: 0.4401 (ptt) REVERT: A 324 MET cc_start: 0.6450 (mmm) cc_final: 0.6115 (mpp) REVERT: A 430 ARG cc_start: 0.7407 (mmm160) cc_final: 0.6821 (mmm160) REVERT: A 695 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: A 874 ASP cc_start: 0.6592 (m-30) cc_final: 0.6390 (m-30) REVERT: A 922 GLN cc_start: 0.6633 (mp10) cc_final: 0.6051 (tt0) REVERT: A 987 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 1044 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 1143 CYS cc_start: 0.7757 (m) cc_final: 0.7332 (m) REVERT: B 37 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8468 (ptt90) REVERT: C 161 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: C 254 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.5074 (m-80) REVERT: C 303 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6932 (m) REVERT: C 463 ILE cc_start: 0.8321 (mp) cc_final: 0.7912 (mp) REVERT: C 541 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6232 (mt-10) REVERT: C 542 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7040 (mmm) REVERT: D 659 LEU cc_start: 0.2232 (OUTLIER) cc_final: 0.1836 (pp) REVERT: D 686 ASP cc_start: 0.7255 (t0) cc_final: 0.6926 (t0) REVERT: D 856 MET cc_start: 0.8447 (ptt) cc_final: 0.8072 (ptt) REVERT: D 932 ASP cc_start: 0.7072 (t0) cc_final: 0.6844 (t70) REVERT: D 1002 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6703 (mp) REVERT: E 58 LEU cc_start: 0.4195 (tt) cc_final: 0.3712 (tp) REVERT: E 81 LEU cc_start: 0.8896 (tt) cc_final: 0.8561 (tt) REVERT: E 91 LEU cc_start: 0.4960 (mt) cc_final: 0.4760 (pp) REVERT: F 254 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.4718 (t80) REVERT: F 464 MET cc_start: 0.6643 (pmm) cc_final: 0.5962 (pmm) REVERT: F 509 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.5209 (t80) REVERT: F 514 GLN cc_start: 0.6323 (mm-40) cc_final: 0.5804 (mt0) outliers start: 127 outliers final: 84 residues processed: 326 average time/residue: 0.1297 time to fit residues: 67.6922 Evaluate side-chains 302 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 204 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1053 CYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 1002 LEU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1025 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1121 ASN Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1198 TRP Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 537 PHE Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 136 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 96 optimal weight: 0.0170 chunk 130 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 237 optimal weight: 1.9990 chunk 260 optimal weight: 0.4980 chunk 199 optimal weight: 6.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS A 955 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.224874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4407 r_free = 0.4407 target = 0.173154 restraints weight = 34931.216| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 3.97 r_work: 0.4063 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22878 Z= 0.111 Angle : 0.585 14.316 30987 Z= 0.290 Chirality : 0.041 0.221 3491 Planarity : 0.004 0.051 3929 Dihedral : 4.289 26.605 3027 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.32 % Allowed : 18.32 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2791 helix: 1.57 (0.15), residues: 1211 sheet: -0.86 (0.23), residues: 505 loop : -1.35 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 356 TYR 0.016 0.001 TYR A 883 PHE 0.013 0.001 PHE F 254 TRP 0.026 0.001 TRP F 406 HIS 0.005 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00242 (22878) covalent geometry : angle 0.58507 (30987) hydrogen bonds : bond 0.03552 ( 996) hydrogen bonds : angle 4.25593 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 216 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6131 (t80) REVERT: A 240 MET cc_start: 0.5147 (tmm) cc_final: 0.4354 (ptt) REVERT: A 324 MET cc_start: 0.6499 (mmm) cc_final: 0.6178 (mpp) REVERT: A 406 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7653 (mt) REVERT: A 430 ARG cc_start: 0.7290 (mmm160) cc_final: 0.6697 (mmm160) REVERT: A 695 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: A 922 GLN cc_start: 0.6503 (mp10) cc_final: 0.5770 (tt0) REVERT: A 1044 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8084 (pp) REVERT: C 161 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: C 254 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5096 (m-80) REVERT: C 303 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6896 (m) REVERT: C 463 ILE cc_start: 0.8249 (mp) cc_final: 0.7889 (mp) REVERT: C 542 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7031 (mmm) REVERT: D 87 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6576 (pptt) REVERT: D 659 LEU cc_start: 0.2290 (OUTLIER) cc_final: 0.1842 (pp) REVERT: D 686 ASP cc_start: 0.7037 (t0) cc_final: 0.6697 (t0) REVERT: D 932 ASP cc_start: 0.6938 (t0) cc_final: 0.6616 (t70) REVERT: E 58 LEU cc_start: 0.4008 (tt) cc_final: 0.3541 (tp) REVERT: F 254 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.4668 (t80) REVERT: F 464 MET cc_start: 0.6664 (pmm) cc_final: 0.5824 (pmm) REVERT: F 509 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.5064 (t80) outliers start: 82 outliers final: 47 residues processed: 278 average time/residue: 0.1246 time to fit residues: 55.6902 Evaluate side-chains 268 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 816 MET Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 959 SER Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 26 optimal weight: 0.3980 chunk 138 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 267 optimal weight: 0.0770 chunk 237 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A 880 HIS A 955 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.225386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.173812 restraints weight = 34905.852| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.45 r_work: 0.4081 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22878 Z= 0.107 Angle : 0.574 13.686 30987 Z= 0.281 Chirality : 0.040 0.211 3491 Planarity : 0.004 0.053 3929 Dihedral : 4.080 22.655 3027 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.15 % Allowed : 18.64 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.16), residues: 2791 helix: 1.75 (0.15), residues: 1215 sheet: -0.93 (0.23), residues: 526 loop : -1.12 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.033 0.001 TYR A 309 PHE 0.014 0.001 PHE D 313 TRP 0.039 0.001 TRP F 406 HIS 0.005 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00240 (22878) covalent geometry : angle 0.57364 (30987) hydrogen bonds : bond 0.03375 ( 996) hydrogen bonds : angle 4.11756 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 224 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 240 MET cc_start: 0.5120 (tmm) cc_final: 0.4340 (ptt) REVERT: A 324 MET cc_start: 0.6438 (mmm) cc_final: 0.6168 (mpp) REVERT: A 378 CYS cc_start: 0.5949 (p) cc_final: 0.5247 (m) REVERT: A 406 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7658 (mt) REVERT: A 430 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6695 (tpt90) REVERT: A 647 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7539 (ptm-80) REVERT: A 1044 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8009 (pp) REVERT: A 1143 CYS cc_start: 0.7748 (m) cc_final: 0.7235 (m) REVERT: B 60 ASP cc_start: 0.6417 (t0) cc_final: 0.6175 (t0) REVERT: C 161 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: C 254 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5125 (m-80) REVERT: C 303 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6952 (m) REVERT: C 463 ILE cc_start: 0.8176 (mp) cc_final: 0.7827 (mp) REVERT: C 542 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7045 (mmm) REVERT: D 87 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6537 (pptt) REVERT: D 534 MET cc_start: 0.3725 (tmm) cc_final: 0.2569 (ptm) REVERT: D 659 LEU cc_start: 0.2212 (OUTLIER) cc_final: 0.1794 (pp) REVERT: D 686 ASP cc_start: 0.7005 (t0) cc_final: 0.6658 (t0) REVERT: D 856 MET cc_start: 0.8617 (ppp) cc_final: 0.8397 (ppp) REVERT: D 932 ASP cc_start: 0.6958 (t0) cc_final: 0.6577 (t70) REVERT: D 987 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6911 (mt) REVERT: E 58 LEU cc_start: 0.4209 (tt) cc_final: 0.3784 (tp) REVERT: F 254 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.4763 (t80) REVERT: F 464 MET cc_start: 0.6558 (pmm) cc_final: 0.5795 (pmm) REVERT: F 509 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5073 (t80) outliers start: 78 outliers final: 53 residues processed: 283 average time/residue: 0.1358 time to fit residues: 61.1015 Evaluate side-chains 276 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 638 PHE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 816 MET Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1198 TRP Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 209 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 88 optimal weight: 0.3980 chunk 210 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS A 955 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.226136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.4455 r_free = 0.4455 target = 0.177016 restraints weight = 34702.195| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 3.64 r_work: 0.4075 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22878 Z= 0.105 Angle : 0.571 13.347 30987 Z= 0.279 Chirality : 0.040 0.232 3491 Planarity : 0.004 0.058 3929 Dihedral : 3.989 22.693 3027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.99 % Allowed : 18.76 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.16), residues: 2791 helix: 1.84 (0.15), residues: 1213 sheet: -0.89 (0.23), residues: 527 loop : -1.07 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.026 0.001 TYR A 309 PHE 0.012 0.001 PHE B 52 TRP 0.035 0.001 TRP F 406 HIS 0.006 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00236 (22878) covalent geometry : angle 0.57075 (30987) hydrogen bonds : bond 0.03223 ( 996) hydrogen bonds : angle 4.05521 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 218 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6017 (t80) REVERT: A 240 MET cc_start: 0.5067 (tmm) cc_final: 0.4300 (ptt) REVERT: A 324 MET cc_start: 0.6430 (mmm) cc_final: 0.6150 (mpp) REVERT: A 378 CYS cc_start: 0.6101 (p) cc_final: 0.5502 (m) REVERT: A 406 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7663 (mt) REVERT: A 430 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6678 (tpt90) REVERT: A 647 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7561 (ptm-80) REVERT: A 1044 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 60 ASP cc_start: 0.6319 (t0) cc_final: 0.6055 (t0) REVERT: C 254 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5123 (m-80) REVERT: C 303 THR cc_start: 0.7231 (OUTLIER) cc_final: 0.6986 (m) REVERT: C 463 ILE cc_start: 0.8141 (mp) cc_final: 0.7799 (mp) REVERT: C 542 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7062 (mmm) REVERT: D 87 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6572 (pptt) REVERT: D 312 MET cc_start: 0.7847 (mtp) cc_final: 0.7056 (ttp) REVERT: D 534 MET cc_start: 0.3926 (tmm) cc_final: 0.2828 (ptm) REVERT: D 659 LEU cc_start: 0.2162 (OUTLIER) cc_final: 0.1758 (pp) REVERT: D 932 ASP cc_start: 0.6939 (t0) cc_final: 0.6634 (t70) REVERT: D 987 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6859 (mt) REVERT: D 1142 LEU cc_start: 0.6726 (tp) cc_final: 0.6414 (tp) REVERT: D 1187 TRP cc_start: 0.6844 (OUTLIER) cc_final: 0.6172 (t60) REVERT: E 58 LEU cc_start: 0.4222 (tt) cc_final: 0.3714 (tp) REVERT: E 91 LEU cc_start: 0.4413 (mm) cc_final: 0.3965 (mt) REVERT: F 254 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.4740 (t80) REVERT: F 464 MET cc_start: 0.6513 (pmm) cc_final: 0.5799 (pmm) REVERT: F 509 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5032 (t80) outliers start: 74 outliers final: 57 residues processed: 271 average time/residue: 0.1368 time to fit residues: 59.4534 Evaluate side-chains 277 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 638 PHE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 816 MET Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1005 MET Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1187 TRP Chi-restraints excluded: chain D residue 1198 TRP Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 191 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 100 optimal weight: 0.0270 chunk 189 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 22 optimal weight: 0.0010 chunk 29 optimal weight: 6.9990 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS A 955 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.225836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.182598 restraints weight = 34682.039| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 2.67 r_work: 0.4107 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22878 Z= 0.107 Angle : 0.584 16.293 30987 Z= 0.282 Chirality : 0.040 0.216 3491 Planarity : 0.004 0.058 3929 Dihedral : 3.943 23.051 3027 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.15 % Allowed : 18.72 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.16), residues: 2791 helix: 1.86 (0.15), residues: 1215 sheet: -0.98 (0.23), residues: 507 loop : -1.01 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.024 0.001 TYR A 309 PHE 0.013 0.001 PHE D 99 TRP 0.035 0.001 TRP F 406 HIS 0.006 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00242 (22878) covalent geometry : angle 0.58363 (30987) hydrogen bonds : bond 0.03253 ( 996) hydrogen bonds : angle 4.04617 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6103 (t80) REVERT: A 240 MET cc_start: 0.5284 (tmm) cc_final: 0.4478 (ptt) REVERT: A 324 MET cc_start: 0.6413 (mmm) cc_final: 0.6163 (mpp) REVERT: A 378 CYS cc_start: 0.5658 (p) cc_final: 0.5072 (m) REVERT: A 406 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 430 ARG cc_start: 0.6962 (mmm160) cc_final: 0.6613 (tpt90) REVERT: A 1044 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8010 (pp) REVERT: B 60 ASP cc_start: 0.6007 (t0) cc_final: 0.5748 (t0) REVERT: C 254 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: C 303 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.7012 (m) REVERT: C 463 ILE cc_start: 0.8053 (mp) cc_final: 0.7691 (mp) REVERT: C 464 MET cc_start: 0.7663 (mmp) cc_final: 0.7435 (mmm) REVERT: C 542 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7075 (mmm) REVERT: D 87 LYS cc_start: 0.7456 (mmtt) cc_final: 0.6694 (pptt) REVERT: D 312 MET cc_start: 0.7419 (mtp) cc_final: 0.6548 (ttp) REVERT: D 534 MET cc_start: 0.4284 (tmm) cc_final: 0.2818 (ptm) REVERT: D 659 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2156 (pp) REVERT: D 932 ASP cc_start: 0.6535 (t0) cc_final: 0.6248 (t70) REVERT: D 987 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6801 (mt) REVERT: D 1142 LEU cc_start: 0.6725 (tp) cc_final: 0.6415 (tp) REVERT: D 1187 TRP cc_start: 0.6685 (OUTLIER) cc_final: 0.6027 (t60) REVERT: E 58 LEU cc_start: 0.4046 (tt) cc_final: 0.3615 (tp) REVERT: E 91 LEU cc_start: 0.4505 (mm) cc_final: 0.3884 (mt) REVERT: F 254 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.4599 (t80) REVERT: F 464 MET cc_start: 0.6464 (pmm) cc_final: 0.5675 (pmm) REVERT: F 509 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5096 (t80) outliers start: 78 outliers final: 62 residues processed: 271 average time/residue: 0.1307 time to fit residues: 56.4899 Evaluate side-chains 281 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 502 HIS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 638 PHE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 816 MET Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1005 MET Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1187 TRP Chi-restraints excluded: chain D residue 1198 TRP Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 158 optimal weight: 0.0670 chunk 210 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 880 HIS A 955 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.225860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.176657 restraints weight = 34791.001| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 3.69 r_work: 0.4079 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22878 Z= 0.107 Angle : 0.588 15.070 30987 Z= 0.282 Chirality : 0.040 0.210 3491 Planarity : 0.004 0.059 3929 Dihedral : 3.925 23.043 3027 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.11 % Allowed : 18.92 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.16), residues: 2791 helix: 1.86 (0.15), residues: 1213 sheet: -1.01 (0.23), residues: 515 loop : -0.98 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 647 TYR 0.023 0.001 TYR A 309 PHE 0.015 0.001 PHE A 243 TRP 0.042 0.001 TRP F 406 HIS 0.006 0.001 HIS D 729 Details of bonding type rmsd covalent geometry : bond 0.00244 (22878) covalent geometry : angle 0.58750 (30987) hydrogen bonds : bond 0.03258 ( 996) hydrogen bonds : angle 4.03599 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5623.30 seconds wall clock time: 96 minutes 48.32 seconds (5808.32 seconds total)