Starting phenix.real_space_refine on Fri Jan 24 21:07:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7w_38129/01_2025/8x7w_38129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7w_38129/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7w_38129/01_2025/8x7w_38129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7w_38129/01_2025/8x7w_38129.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7w_38129/01_2025/8x7w_38129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7w_38129/01_2025/8x7w_38129.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: 13.03, per 1000 atoms: 0.58 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: 5.62 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.69 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: 8.61 Time building geometry restraints manager: 6.51 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: 3.400 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 49.100 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.120 ------------------------------------------------------------------------------- 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= 0.188 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 : 7.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP A1161 HIS 0.006 0.001 HIS D 863 PHE 0.013 0.001 PHE D 99 TYR 0.019 0.001 TYR A 70 ARG 0.007 0.000 ARG E 67 *********************** 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 : 2.735 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: 0.6154 (m100) REVERT: A 874 ASP cc_start: 0.6753 (m-30) cc_final: 0.6237 (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: 0.3845 time to fit residues: 142.4905 Evaluate side-chains 207 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 219 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 0.0010 chunk 163 optimal weight: 0.0980 chunk 254 optimal weight: 10.0000 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 F 495 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.226766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.187093 restraints weight = 34394.936| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 2.96 r_work: 0.4108 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22878 Z= 0.179 Angle : 0.588 7.645 30987 Z= 0.299 Chirality : 0.042 0.162 3491 Planarity : 0.004 0.091 3929 Dihedral : 3.902 33.534 3027 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 12.29 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2791 helix: 2.08 (0.15), residues: 1219 sheet: -0.78 (0.23), residues: 527 loop : -0.97 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 406 HIS 0.007 0.001 HIS A 238 PHE 0.014 0.001 PHE D 60 TYR 0.031 0.001 TYR A 883 ARG 0.008 0.000 ARG D 855 *********************** 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 276 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.4922 (tmm) cc_final: 0.4474 (ptt) REVERT: A 406 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7711 (mt) REVERT: A 430 ARG cc_start: 0.6793 (tpt90) cc_final: 0.6567 (tpt90) REVERT: A 540 TRP cc_start: 0.6893 (m100) cc_final: 0.6063 (m100) REVERT: A 874 ASP cc_start: 0.6627 (m-30) cc_final: 0.6312 (m-30) REVERT: A 1044 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7875 (pp) REVERT: B 37 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7916 (ptt90) REVERT: C 161 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: C 254 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: C 463 ILE cc_start: 0.8018 (mp) cc_final: 0.7777 (mp) REVERT: D 87 LYS cc_start: 0.7298 (mmtt) cc_final: 0.6572 (pptt) REVERT: D 932 ASP cc_start: 0.6504 (t0) cc_final: 0.6181 (t70) REVERT: D 1044 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5477 (pp) REVERT: E 81 LEU cc_start: 0.8777 (pp) cc_final: 0.8570 (tt) REVERT: F 254 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.4903 (t80) REVERT: F 456 GLU cc_start: 0.5447 (tm-30) cc_final: 0.4888 (tp30) REVERT: F 509 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5031 (t80) outliers start: 40 outliers final: 12 residues processed: 260 average time/residue: 0.3432 time to fit residues: 140.3396 Evaluate side-chains 225 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 A1200 ASN F 564 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.226377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.173997 restraints weight = 34331.310| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.80 r_work: 0.4087 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22878 Z= 0.181 Angle : 0.559 13.863 30987 Z= 0.280 Chirality : 0.041 0.183 3491 Planarity : 0.004 0.048 3929 Dihedral : 3.893 30.814 3027 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.83 % Allowed : 12.58 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2791 helix: 2.03 (0.15), residues: 1213 sheet: -0.71 (0.23), residues: 525 loop : -0.92 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 406 HIS 0.004 0.001 HIS A 627 PHE 0.013 0.001 PHE D 313 TYR 0.019 0.001 TYR A 883 ARG 0.005 0.000 ARG D 617 *********************** 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 292 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5931 (t80) REVERT: A 324 MET cc_start: 0.6199 (mmm) cc_final: 0.5836 (mpp) REVERT: A 406 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7716 (mt) REVERT: A 540 TRP cc_start: 0.6848 (m100) cc_final: 0.5999 (m100) REVERT: A 874 ASP cc_start: 0.6755 (m-30) cc_final: 0.6518 (m-30) REVERT: A 918 LEU cc_start: 0.7909 (tp) cc_final: 0.7683 (tt) REVERT: A 920 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 1044 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7852 (pp) REVERT: B 37 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8203 (ptt90) REVERT: C 161 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: C 254 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: C 463 ILE cc_start: 0.8146 (mp) cc_final: 0.7829 (mp) REVERT: C 496 MET cc_start: 0.7743 (mmt) cc_final: 0.7505 (mmm) REVERT: C 542 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6646 (mmm) REVERT: D 280 ARG cc_start: 0.3490 (ttt180) cc_final: 0.3149 (ttt180) REVERT: D 932 ASP cc_start: 0.6873 (t0) cc_final: 0.6496 (t70) REVERT: E 81 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8607 (tt) REVERT: F 254 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.4946 (t80) REVERT: F 509 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.4983 (t80) outliers start: 70 outliers final: 31 residues processed: 268 average time/residue: 0.3404 time to fit residues: 144.2153 Evaluate side-chains 246 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 510 LEU 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 920 VAL 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 1079 ASP Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1118 LEU 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 336 PHE Chi-restraints excluded: chain C residue 339 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 940 CYS 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 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 212 optimal weight: 6.9990 chunk 274 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 C 433 ASN D1012 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.224834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.175422 restraints weight = 34705.496| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 3.10 r_work: 0.4087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22878 Z= 0.211 Angle : 0.577 9.641 30987 Z= 0.288 Chirality : 0.042 0.201 3491 Planarity : 0.004 0.046 3929 Dihedral : 4.013 30.676 3027 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.15 % Allowed : 13.95 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2791 helix: 1.89 (0.15), residues: 1211 sheet: -0.64 (0.23), residues: 529 loop : -1.04 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 406 HIS 0.004 0.001 HIS A 629 PHE 0.012 0.001 PHE F 254 TYR 0.017 0.001 TYR A 883 ARG 0.014 0.000 ARG A 430 *********************** 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 301 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 223 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5925 (t80) REVERT: A 240 MET cc_start: 0.4720 (tmm) cc_final: 0.4424 (ptt) REVERT: A 406 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7732 (mt) REVERT: A 540 TRP cc_start: 0.6929 (m100) cc_final: 0.6013 (m100) REVERT: A 794 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6272 (p) REVERT: A 874 ASP cc_start: 0.6635 (m-30) cc_final: 0.6417 (m-30) REVERT: A 1044 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7873 (pp) REVERT: B 37 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8194 (ptt90) REVERT: B 53 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: C 161 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: C 254 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5122 (m-80) REVERT: C 463 ILE cc_start: 0.8158 (mp) cc_final: 0.7720 (mp) REVERT: C 464 MET cc_start: 0.7656 (mmp) cc_final: 0.7361 (mmm) REVERT: C 542 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6764 (mmm) REVERT: D 659 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1806 (pp) REVERT: D 729 HIS cc_start: 0.5385 (m170) cc_final: 0.5140 (m170) REVERT: D 932 ASP cc_start: 0.6863 (t0) cc_final: 0.6518 (t70) REVERT: E 81 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8474 (tt) REVERT: F 251 PRO cc_start: 0.6451 (Cg_exo) cc_final: 0.6249 (Cg_endo) REVERT: F 254 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.4612 (t80) REVERT: F 456 GLU cc_start: 0.5473 (tm-30) cc_final: 0.5067 (tm-30) REVERT: F 464 MET cc_start: 0.6192 (pmm) cc_final: 0.4914 (pmm) REVERT: F 485 TRP cc_start: 0.5056 (m100) cc_final: 0.4706 (m100) REVERT: F 509 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.4998 (t80) REVERT: F 514 GLN cc_start: 0.6582 (mm-40) cc_final: 0.5877 (mt0) outliers start: 78 outliers final: 48 residues processed: 278 average time/residue: 0.3503 time to fit residues: 154.3514 Evaluate side-chains 263 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 510 LEU Chi-restraints excluded: chain A residue 545 VAL 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 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 1053 CYS 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 1140 MET Chi-restraints excluded: chain A residue 1170 LEU 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 53 TYR 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 304 CYS 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 339 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 657 VAL Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 816 MET 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 982 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 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 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 174 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 ASN E 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.225592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4443 r_free = 0.4443 target = 0.174921 restraints weight = 34996.418| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.32 r_work: 0.4081 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22878 Z= 0.183 Angle : 0.556 10.361 30987 Z= 0.276 Chirality : 0.041 0.168 3491 Planarity : 0.004 0.052 3929 Dihedral : 3.955 29.829 3027 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.52 % Allowed : 14.84 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2791 helix: 1.89 (0.15), residues: 1212 sheet: -0.61 (0.23), residues: 527 loop : -1.01 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 303 HIS 0.004 0.001 HIS D 863 PHE 0.013 0.001 PHE D 313 TYR 0.016 0.001 TYR A 883 ARG 0.009 0.000 ARG B 118 *********************** 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 308 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 221 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6057 (t80) REVERT: A 324 MET cc_start: 0.6480 (mmm) cc_final: 0.6117 (mpp) REVERT: A 406 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7667 (mt) REVERT: A 540 TRP cc_start: 0.6887 (m100) cc_final: 0.5960 (m100) REVERT: A 794 THR cc_start: 0.6519 (OUTLIER) cc_final: 0.6298 (p) REVERT: A 920 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 1044 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 1143 CYS cc_start: 0.7794 (m) cc_final: 0.7299 (m) REVERT: B 37 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8203 (ptt90) REVERT: B 60 ASP cc_start: 0.6904 (t0) cc_final: 0.6675 (t0) REVERT: C 161 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: C 254 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: C 463 ILE cc_start: 0.8222 (mp) cc_final: 0.7886 (mp) REVERT: C 542 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6912 (mmm) REVERT: D 659 LEU cc_start: 0.2255 (OUTLIER) cc_final: 0.1784 (pp) REVERT: D 729 HIS cc_start: 0.5345 (m170) cc_final: 0.5095 (m170) REVERT: D 932 ASP cc_start: 0.6800 (t0) cc_final: 0.6440 (t70) REVERT: E 81 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8477 (tt) REVERT: F 251 PRO cc_start: 0.6547 (Cg_exo) cc_final: 0.6344 (Cg_endo) REVERT: F 254 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.4481 (t80) REVERT: F 485 TRP cc_start: 0.5131 (m100) cc_final: 0.4899 (m100) REVERT: F 509 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5053 (t80) REVERT: F 514 GLN cc_start: 0.6639 (mm-40) cc_final: 0.5974 (mt0) outliers start: 87 outliers final: 56 residues processed: 283 average time/residue: 0.3296 time to fit residues: 148.5062 Evaluate side-chains 269 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 2.336 ------------------------------------------------------------------------------- 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 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 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 879 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 920 VAL 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 1053 CYS 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 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 304 CYS 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 339 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 C residue 566 SER Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 816 MET 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 982 LEU 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 1140 MET Chi-restraints excluded: chain E residue 81 LEU 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 479 MET Chi-restraints excluded: chain F residue 496 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 207 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 148 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN A 838 ASN A 880 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN D 782 HIS E 33 GLN F 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.220626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.177258 restraints weight = 34963.083| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.92 r_work: 0.4021 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22878 Z= 0.339 Angle : 0.699 18.191 30987 Z= 0.350 Chirality : 0.045 0.171 3491 Planarity : 0.005 0.058 3929 Dihedral : 4.610 33.843 3027 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.84 % Allowed : 16.01 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2791 helix: 1.33 (0.15), residues: 1214 sheet: -1.16 (0.22), residues: 547 loop : -1.22 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 406 HIS 0.009 0.001 HIS D1012 PHE 0.021 0.002 PHE F 395 TYR 0.027 0.002 TYR A 70 ARG 0.006 0.001 ARG F 404 *********************** 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 309 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 214 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6201 (t80) REVERT: A 240 MET cc_start: 0.5319 (ptt) cc_final: 0.4072 (ppp) REVERT: A 305 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 324 MET cc_start: 0.6499 (mmm) cc_final: 0.6218 (mpp) REVERT: A 430 ARG cc_start: 0.7621 (mmm160) cc_final: 0.7170 (mmm160) REVERT: A 540 TRP cc_start: 0.6941 (m100) cc_final: 0.6508 (m100) REVERT: A 904 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6512 (m110) REVERT: A 920 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 1044 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 1143 CYS cc_start: 0.7752 (m) cc_final: 0.7363 (m) REVERT: B 37 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8420 (ptt90) REVERT: C 161 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: C 303 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6618 (m) REVERT: C 463 ILE cc_start: 0.8281 (mp) cc_final: 0.7904 (mp) REVERT: C 542 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6920 (mmm) REVERT: D 659 LEU cc_start: 0.2534 (OUTLIER) cc_final: 0.2028 (pp) REVERT: D 686 ASP cc_start: 0.7067 (t0) cc_final: 0.6804 (t0) REVERT: F 254 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.4678 (t80) REVERT: F 485 TRP cc_start: 0.5423 (m100) cc_final: 0.5079 (m100) REVERT: F 509 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5208 (t80) REVERT: F 514 GLN cc_start: 0.6601 (mm-40) cc_final: 0.5949 (mt0) outliers start: 95 outliers final: 63 residues processed: 289 average time/residue: 0.3438 time to fit residues: 157.3639 Evaluate side-chains 280 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 205 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 505 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 904 ASN Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 920 VAL 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 1044 LEU 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 1129 LEU Chi-restraints excluded: chain A residue 1131 GLN 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 303 THR Chi-restraints excluded: chain C residue 304 CYS 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 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 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 947 LEU 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 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 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 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 206 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.223146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171232 restraints weight = 34731.197| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 4.26 r_work: 0.4017 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22878 Z= 0.218 Angle : 0.612 16.126 30987 Z= 0.303 Chirality : 0.042 0.237 3491 Planarity : 0.004 0.055 3929 Dihedral : 4.374 32.814 3027 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.76 % Allowed : 16.90 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2791 helix: 1.54 (0.15), residues: 1210 sheet: -1.01 (0.22), residues: 533 loop : -1.20 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 406 HIS 0.004 0.001 HIS A 629 PHE 0.014 0.001 PHE F 254 TYR 0.018 0.002 TYR A 70 ARG 0.006 0.000 ARG D 617 *********************** 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 303 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 210 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6175 (t80) REVERT: A 96 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5599 (mt) REVERT: A 324 MET cc_start: 0.6531 (mmm) cc_final: 0.6203 (mpp) REVERT: A 406 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7698 (mt) REVERT: A 430 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7114 (mmm160) REVERT: A 643 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5791 (mm-30) REVERT: A 695 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: A 883 TYR cc_start: 0.6244 (m-80) cc_final: 0.6032 (m-80) REVERT: A 920 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7534 (p) REVERT: A 1044 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7997 (pp) REVERT: A 1143 CYS cc_start: 0.7767 (m) cc_final: 0.7276 (m) REVERT: B 37 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8443 (ptt90) REVERT: B 121 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6998 (ptm160) REVERT: C 161 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: C 254 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5040 (m-80) REVERT: C 303 THR cc_start: 0.7101 (OUTLIER) cc_final: 0.6833 (m) REVERT: C 463 ILE cc_start: 0.8367 (mp) cc_final: 0.8029 (mp) REVERT: C 542 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7012 (mmm) REVERT: D 312 MET cc_start: 0.7115 (mtp) cc_final: 0.6605 (ttt) REVERT: D 534 MET cc_start: 0.3598 (tmm) cc_final: 0.2805 (ptm) REVERT: D 659 LEU cc_start: 0.2399 (OUTLIER) cc_final: 0.1979 (pp) REVERT: D 686 ASP cc_start: 0.7032 (t0) cc_final: 0.6723 (t0) REVERT: E 81 LEU cc_start: 0.8847 (tt) cc_final: 0.8495 (tt) REVERT: F 254 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.4779 (t80) REVERT: F 464 MET cc_start: 0.6512 (pmm) cc_final: 0.5614 (pmm) REVERT: F 509 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5140 (t80) REVERT: F 514 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6057 (mt0) outliers start: 93 outliers final: 62 residues processed: 284 average time/residue: 0.3367 time to fit residues: 152.8296 Evaluate side-chains 275 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 96 ILE 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 417 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 541 ASN 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 861 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 920 VAL 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 1010 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 1129 LEU Chi-restraints excluded: chain A residue 1131 GLN 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 53 TYR Chi-restraints excluded: chain B residue 121 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 296 SER 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 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 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 394 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 816 MET Chi-restraints excluded: chain D residue 873 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 982 LEU Chi-restraints excluded: chain D residue 985 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 541 ASN A 838 ASN A 880 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.224260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.178934 restraints weight = 34675.434| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.55 r_work: 0.4098 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22878 Z= 0.187 Angle : 0.594 15.678 30987 Z= 0.292 Chirality : 0.041 0.252 3491 Planarity : 0.004 0.057 3929 Dihedral : 4.201 25.826 3027 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.56 % Allowed : 17.47 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2791 helix: 1.67 (0.15), residues: 1211 sheet: -0.93 (0.23), residues: 529 loop : -1.18 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 340 HIS 0.004 0.001 HIS A 627 PHE 0.013 0.001 PHE F 254 TYR 0.025 0.001 TYR A 309 ARG 0.009 0.000 ARG D 356 *********************** 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 299 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 211 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6230 (t80) REVERT: A 240 MET cc_start: 0.4629 (ptt) cc_final: 0.4364 (ptt) REVERT: A 324 MET cc_start: 0.6476 (mmm) cc_final: 0.6190 (mpp) REVERT: A 406 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 430 ARG cc_start: 0.7469 (mmm160) cc_final: 0.6912 (mmm160) REVERT: A 647 ARG cc_start: 0.8008 (mtp-110) cc_final: 0.7501 (ptm-80) REVERT: A 695 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: A 920 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7717 (p) REVERT: A 1044 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7973 (pp) REVERT: A 1143 CYS cc_start: 0.7526 (m) cc_final: 0.7138 (m) REVERT: B 37 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8365 (ptt90) REVERT: B 121 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7039 (ptm160) REVERT: C 161 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: C 254 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5116 (m-80) REVERT: C 303 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6979 (m) REVERT: C 463 ILE cc_start: 0.8264 (mp) cc_final: 0.7912 (mp) REVERT: C 542 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6904 (mmm) REVERT: D 87 LYS cc_start: 0.7442 (mmtt) cc_final: 0.6718 (pptt) REVERT: D 312 MET cc_start: 0.7038 (mtp) cc_final: 0.6230 (ttp) REVERT: D 534 MET cc_start: 0.4039 (tmm) cc_final: 0.2862 (ptm) REVERT: D 659 LEU cc_start: 0.2647 (OUTLIER) cc_final: 0.2095 (pp) REVERT: D 686 ASP cc_start: 0.6908 (t0) cc_final: 0.6629 (t0) REVERT: E 58 LEU cc_start: 0.4004 (tt) cc_final: 0.3447 (tp) REVERT: E 91 LEU cc_start: 0.4597 (mm) cc_final: 0.4396 (pp) REVERT: F 254 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.4689 (t80) REVERT: F 464 MET cc_start: 0.6626 (pmm) cc_final: 0.5760 (pmm) REVERT: F 509 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5109 (t80) REVERT: F 514 GLN cc_start: 0.6754 (mm-40) cc_final: 0.6198 (mt0) outliers start: 88 outliers final: 67 residues processed: 276 average time/residue: 0.3419 time to fit residues: 151.0013 Evaluate side-chains 287 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 2.367 ------------------------------------------------------------------------------- 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 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 541 ASN 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 861 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 920 VAL 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 1004 LEU Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU 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 1129 LEU Chi-restraints excluded: chain A residue 1131 GLN 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 53 TYR Chi-restraints excluded: chain B residue 121 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 296 SER 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 315 THR 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 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 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 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 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 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 364 LEU 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 Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 274 optimal weight: 0.2980 chunk 222 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A 880 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.224041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.175987 restraints weight = 34488.343| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.96 r_work: 0.4077 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22878 Z= 0.195 Angle : 0.601 15.322 30987 Z= 0.295 Chirality : 0.041 0.215 3491 Planarity : 0.004 0.059 3929 Dihedral : 4.191 24.903 3027 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.68 % Allowed : 17.43 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2791 helix: 1.67 (0.15), residues: 1213 sheet: -0.97 (0.23), residues: 517 loop : -1.16 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 406 HIS 0.004 0.001 HIS A 627 PHE 0.028 0.001 PHE D 99 TYR 0.028 0.001 TYR A 309 ARG 0.008 0.000 ARG E 67 *********************** 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 295 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 204 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6070 (t80) REVERT: A 240 MET cc_start: 0.4498 (ptt) cc_final: 0.4019 (ppp) REVERT: A 324 MET cc_start: 0.6408 (mmm) cc_final: 0.6139 (mpp) REVERT: A 406 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7683 (mt) REVERT: A 430 ARG cc_start: 0.7502 (mmm160) cc_final: 0.6885 (mmm160) REVERT: A 695 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: A 920 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7615 (p) REVERT: A 1044 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7977 (pp) REVERT: B 37 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8401 (ptt90) REVERT: B 121 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7093 (ptm160) REVERT: C 161 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: C 254 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5112 (m-80) REVERT: C 303 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6916 (m) REVERT: C 463 ILE cc_start: 0.8209 (mp) cc_final: 0.7843 (mp) REVERT: C 542 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6985 (mmm) REVERT: D 87 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6612 (pptt) REVERT: D 312 MET cc_start: 0.7303 (mtp) cc_final: 0.6618 (ttt) REVERT: D 534 MET cc_start: 0.3975 (tmm) cc_final: 0.2682 (ptm) REVERT: D 659 LEU cc_start: 0.2462 (OUTLIER) cc_final: 0.1978 (pp) REVERT: D 686 ASP cc_start: 0.6970 (t0) cc_final: 0.6661 (t0) REVERT: D 1142 LEU cc_start: 0.6845 (tp) cc_final: 0.6539 (tp) REVERT: E 58 LEU cc_start: 0.4093 (tt) cc_final: 0.3539 (tp) REVERT: E 91 LEU cc_start: 0.4350 (mm) cc_final: 0.4091 (pp) REVERT: F 254 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.4728 (t80) REVERT: F 464 MET cc_start: 0.6538 (pmm) cc_final: 0.5711 (pmm) REVERT: F 509 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5064 (t80) REVERT: F 514 GLN cc_start: 0.6802 (mm-40) cc_final: 0.6250 (mt0) outliers start: 91 outliers final: 72 residues processed: 274 average time/residue: 0.3324 time to fit residues: 145.1280 Evaluate side-chains 285 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 199 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 510 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 541 ASN 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 861 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 920 VAL 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 1010 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1044 LEU 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 1129 LEU Chi-restraints excluded: chain A residue 1131 GLN 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 53 TYR Chi-restraints excluded: chain B residue 121 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 296 SER 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 315 THR 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 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 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 816 MET Chi-restraints excluded: chain D residue 873 LEU 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 1011 THR 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 1131 GLN Chi-restraints excluded: chain D residue 1140 MET 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 364 LEU 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 Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 269 optimal weight: 4.9990 chunk 172 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 137 optimal weight: 0.1980 chunk 198 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 279 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.226268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.175855 restraints weight = 35106.880| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.79 r_work: 0.4077 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2615 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= 0.154 Angle : 0.573 14.845 30987 Z= 0.280 Chirality : 0.040 0.213 3491 Planarity : 0.004 0.061 3929 Dihedral : 4.005 23.069 3027 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.03 % Allowed : 18.03 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2791 helix: 1.80 (0.15), residues: 1213 sheet: -0.71 (0.23), residues: 513 loop : -1.11 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 406 HIS 0.003 0.001 HIS F 495 PHE 0.026 0.001 PHE D 99 TYR 0.025 0.001 TYR A 309 ARG 0.008 0.000 ARG A 647 ********************** 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 287 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6068 (t80) REVERT: A 240 MET cc_start: 0.4448 (ptt) cc_final: 0.3914 (ppp) REVERT: A 324 MET cc_start: 0.6396 (mmm) cc_final: 0.6097 (mpp) REVERT: A 406 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7620 (mt) REVERT: A 430 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6686 (mmm160) REVERT: A 920 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7456 (p) REVERT: A 1044 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8022 (pp) REVERT: A 1143 CYS cc_start: 0.7845 (m) cc_final: 0.7485 (m) REVERT: B 121 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7072 (mtp180) REVERT: C 254 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5076 (m-80) REVERT: C 303 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6949 (m) REVERT: C 463 ILE cc_start: 0.8259 (mp) cc_final: 0.7879 (mp) REVERT: C 464 MET cc_start: 0.7901 (mmp) cc_final: 0.7662 (mmm) REVERT: C 542 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7037 (mmm) REVERT: D 87 LYS cc_start: 0.7041 (mmtt) cc_final: 0.6529 (pptt) REVERT: D 312 MET cc_start: 0.7508 (mtp) cc_final: 0.6873 (ttt) REVERT: D 534 MET cc_start: 0.4232 (tmm) cc_final: 0.3340 (ptm) REVERT: D 659 LEU cc_start: 0.2230 (OUTLIER) cc_final: 0.1831 (pp) REVERT: D 987 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6956 (mt) REVERT: D 1142 LEU cc_start: 0.6802 (tp) cc_final: 0.6466 (tp) REVERT: E 58 LEU cc_start: 0.4066 (tt) cc_final: 0.3548 (tp) REVERT: E 91 LEU cc_start: 0.4273 (mm) cc_final: 0.3937 (pp) REVERT: F 254 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.4706 (t80) REVERT: F 464 MET cc_start: 0.6458 (pmm) cc_final: 0.5689 (pmm) REVERT: F 509 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5028 (t80) REVERT: F 514 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6271 (mt0) outliers start: 75 outliers final: 57 residues processed: 268 average time/residue: 0.3337 time to fit residues: 143.7703 Evaluate side-chains 275 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 206 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 541 ASN 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 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 920 VAL 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 1010 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 1174 VAL Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 121 ARG 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 304 CYS Chi-restraints excluded: chain C residue 315 THR 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 274 ARG Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 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 1011 THR 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 1140 MET Chi-restraints excluded: chain D residue 1198 TRP 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 364 LEU Chi-restraints excluded: chain F residue 403 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 277 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- 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 = 0.4889 r_free = 0.4889 target = 0.223325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4396 r_free = 0.4396 target = 0.173145 restraints weight = 34797.450| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 4.17 r_work: 0.4021 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22878 Z= 0.237 Angle : 0.630 14.789 30987 Z= 0.309 Chirality : 0.042 0.216 3491 Planarity : 0.004 0.060 3929 Dihedral : 4.195 24.722 3027 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.36 % Allowed : 18.20 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2791 helix: 1.65 (0.15), residues: 1213 sheet: -1.20 (0.22), residues: 557 loop : -1.09 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 406 HIS 0.005 0.001 HIS A 955 PHE 0.025 0.002 PHE D 99 TYR 0.022 0.002 TYR A 309 ARG 0.007 0.000 ARG A 647 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12151.21 seconds wall clock time: 217 minutes 20.85 seconds (13040.85 seconds total)