Starting phenix.real_space_refine on Thu Jun 19 11:05:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7w_38129/06_2025/8x7w_38129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7w_38129/06_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_38129/06_2025/8x7w_38129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7w_38129/06_2025/8x7w_38129.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7w_38129/06_2025/8x7w_38129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7w_38129/06_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.93, per 1000 atoms: 0.62 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: 5.77 Conformation dependent library (CDL) restraints added in 2.9 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: 2.93 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: 9.15 Time building geometry restraints manager: 6.91 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: 4.180 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 53.110 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22878 Z= 0.141 Angle : 0.558 7.402 30987 Z= 0.311 Chirality : 0.038 0.167 3491 Planarity : 0.006 0.302 3929 Dihedral : 13.057 88.851 8386 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.78 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 Details of bonding type rmsd hydrogen bonds : bond 0.18383 ( 996) hydrogen bonds : angle 6.16910 ( 2880) covalent geometry : bond 0.00287 (22878) covalent geometry : angle 0.55792 (30987) *********************** 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 : 2.348 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: 0.3361 time to fit residues: 124.4219 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 : 2.479 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.187650 restraints weight = 34395.382| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.88 r_work: 0.4120 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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= 0.126 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 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 996) hydrogen bonds : angle 4.65776 ( 2880) covalent geometry : bond 0.00274 (22878) covalent geometry : angle 0.58752 (30987) *********************** 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 : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.4919 (tmm) cc_final: 0.4475 (ptt) REVERT: A 406 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7703 (mt) REVERT: A 430 ARG cc_start: 0.6758 (tpt90) cc_final: 0.6528 (tpt90) REVERT: A 540 TRP cc_start: 0.6890 (m100) cc_final: 0.6065 (m100) REVERT: A 874 ASP cc_start: 0.6610 (m-30) cc_final: 0.6296 (m-30) REVERT: A 1044 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7873 (pp) REVERT: B 37 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7913 (ptt90) REVERT: C 161 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7566 (tp30) REVERT: C 254 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5136 (m-80) REVERT: C 463 ILE cc_start: 0.8008 (mp) cc_final: 0.7768 (mp) REVERT: D 87 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6577 (pptt) REVERT: D 932 ASP cc_start: 0.6471 (t0) cc_final: 0.6150 (t70) REVERT: D 1044 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5468 (pp) REVERT: E 81 LEU cc_start: 0.8770 (pp) cc_final: 0.8568 (tt) REVERT: F 254 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.4899 (t80) REVERT: F 456 GLU cc_start: 0.5439 (tm-30) cc_final: 0.4885 (tp30) REVERT: F 509 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5016 (t80) outliers start: 40 outliers final: 12 residues processed: 260 average time/residue: 0.3422 time to fit residues: 140.9976 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 : 2.500 ------------------------------------------------------------------------------- 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: 0.9990 chunk 207 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 D1012 HIS F 564 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.225995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.172630 restraints weight = 34331.459| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.70 r_work: 0.4094 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1420 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= 0.129 Angle : 0.565 13.975 30987 Z= 0.283 Chirality : 0.041 0.196 3491 Planarity : 0.004 0.048 3929 Dihedral : 3.921 30.904 3027 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.79 % Allowed : 12.74 % Favored : 84.47 % 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: 0.57 (0.16), residues: 2791 helix: 2.03 (0.15), residues: 1209 sheet: -0.75 (0.23), residues: 527 loop : -0.94 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 406 HIS 0.004 0.001 HIS A 627 PHE 0.015 0.001 PHE D 313 TYR 0.020 0.001 TYR A 883 ARG 0.004 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 996) hydrogen bonds : angle 4.39889 ( 2880) covalent geometry : bond 0.00292 (22878) covalent geometry : angle 0.56482 (30987) *********************** 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 291 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5896 (t80) REVERT: A 324 MET cc_start: 0.6229 (mmm) cc_final: 0.5850 (mpp) REVERT: A 406 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 540 TRP cc_start: 0.6843 (m100) cc_final: 0.5923 (m100) REVERT: A 874 ASP cc_start: 0.6727 (m-30) cc_final: 0.6481 (m-30) REVERT: A 918 LEU cc_start: 0.7911 (tp) cc_final: 0.7682 (tt) REVERT: A 920 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (p) REVERT: A 1044 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 37 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8195 (ptt90) REVERT: C 161 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: C 254 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: C 463 ILE cc_start: 0.8167 (mp) cc_final: 0.7836 (mp) REVERT: C 496 MET cc_start: 0.7733 (mmt) cc_final: 0.7472 (mmm) REVERT: D 280 ARG cc_start: 0.3619 (ttt180) cc_final: 0.3277 (ttt180) REVERT: D 932 ASP cc_start: 0.6847 (t0) cc_final: 0.6465 (t70) REVERT: D 1017 MET cc_start: 0.7337 (mpp) cc_final: 0.6979 (mpp) REVERT: E 81 LEU cc_start: 0.8857 (pp) cc_final: 0.8602 (tt) REVERT: F 254 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.4938 (t80) REVERT: F 509 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.4974 (t80) outliers start: 69 outliers final: 29 residues processed: 270 average time/residue: 0.4017 time to fit residues: 174.7394 Evaluate side-chains 241 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 2.978 ------------------------------------------------------------------------------- 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 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 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 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 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: 4.9990 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 128 optimal weight: 0.0170 chunk 239 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 E 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.227912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4416 r_free = 0.4416 target = 0.175081 restraints weight = 34650.978| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 4.08 r_work: 0.4091 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22878 Z= 0.105 Angle : 0.534 10.310 30987 Z= 0.265 Chirality : 0.040 0.211 3491 Planarity : 0.004 0.044 3929 Dihedral : 3.803 28.734 3027 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.59 % Allowed : 13.83 % Favored : 83.58 % 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: 0.71 (0.16), residues: 2791 helix: 2.06 (0.15), residues: 1214 sheet: -0.43 (0.23), residues: 531 loop : -0.92 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 303 HIS 0.004 0.001 HIS D 863 PHE 0.013 0.001 PHE D 313 TYR 0.019 0.001 TYR A 883 ARG 0.010 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 996) hydrogen bonds : angle 4.17379 ( 2880) covalent geometry : bond 0.00227 (22878) covalent geometry : angle 0.53372 (30987) *********************** 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 291 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 227 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5879 (t80) REVERT: A 240 MET cc_start: 0.4660 (tmm) cc_final: 0.4382 (ptt) REVERT: A 324 MET cc_start: 0.6484 (mmm) cc_final: 0.6022 (mpp) REVERT: A 406 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7582 (mt) REVERT: A 540 TRP cc_start: 0.6768 (m100) cc_final: 0.5955 (m100) REVERT: A 794 THR cc_start: 0.6517 (OUTLIER) cc_final: 0.6287 (p) REVERT: A 918 LEU cc_start: 0.7873 (tp) cc_final: 0.7624 (tt) REVERT: A 1044 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7884 (pp) REVERT: A 1143 CYS cc_start: 0.7793 (m) cc_final: 0.7259 (m) REVERT: B 60 ASP cc_start: 0.6706 (t0) cc_final: 0.6478 (t0) REVERT: C 254 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: C 463 ILE cc_start: 0.8132 (mp) cc_final: 0.7748 (mp) REVERT: C 542 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6583 (mmm) REVERT: D 659 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2342 (pp) REVERT: E 81 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8546 (tt) REVERT: F 162 GLN cc_start: 0.4058 (OUTLIER) cc_final: 0.3679 (mm110) REVERT: F 254 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.4503 (t80) REVERT: F 464 MET cc_start: 0.6122 (pmm) cc_final: 0.4921 (pmm) REVERT: F 485 TRP cc_start: 0.5614 (m100) cc_final: 0.5376 (m100) REVERT: F 509 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.4967 (t80) REVERT: F 514 GLN cc_start: 0.6484 (mm-40) cc_final: 0.5817 (mt0) outliers start: 64 outliers final: 35 residues processed: 269 average time/residue: 0.3281 time to fit residues: 140.7984 Evaluate side-chains 249 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 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 904 ASN Chi-restraints excluded: chain A residue 959 SER 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 1140 MET Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP 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 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 971 LEU Chi-restraints excluded: chain D residue 982 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 162 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 174 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 C 433 ASN ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 HIS D 904 ASN E 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.222247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.172408 restraints weight = 34684.554| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 3.58 r_work: 0.4020 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22878 Z= 0.194 Angle : 0.637 9.952 30987 Z= 0.321 Chirality : 0.043 0.167 3491 Planarity : 0.004 0.052 3929 Dihedral : 4.277 31.410 3027 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.88 % Allowed : 14.72 % Favored : 81.40 % 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: 0.23 (0.16), residues: 2791 helix: 1.69 (0.15), residues: 1208 sheet: -0.82 (0.23), residues: 537 loop : -1.10 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 406 HIS 0.007 0.001 HIS D1012 PHE 0.018 0.002 PHE F 395 TYR 0.023 0.002 TYR A 426 ARG 0.004 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 996) hydrogen bonds : angle 4.50430 ( 2880) covalent geometry : bond 0.00459 (22878) covalent geometry : angle 0.63666 (30987) *********************** 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: 96 poor density : 212 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6322 (t80) REVERT: A 406 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7615 (mt) REVERT: A 430 ARG cc_start: 0.7392 (tpp-160) cc_final: 0.7166 (mmm160) REVERT: A 540 TRP cc_start: 0.6867 (m100) cc_final: 0.5996 (m100) REVERT: A 794 THR cc_start: 0.6542 (OUTLIER) cc_final: 0.6314 (p) REVERT: A 920 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (p) REVERT: A 1044 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8029 (pp) REVERT: B 37 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8273 (ptt90) REVERT: C 161 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: C 463 ILE cc_start: 0.8306 (mp) cc_final: 0.7953 (mp) REVERT: C 542 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6828 (mmm) REVERT: D 659 LEU cc_start: 0.2186 (OUTLIER) cc_final: 0.1800 (pp) REVERT: E 81 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8565 (tt) REVERT: F 254 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.4676 (t80) REVERT: F 509 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.5085 (t80) REVERT: F 514 GLN cc_start: 0.6655 (mm-40) cc_final: 0.5984 (mt0) outliers start: 96 outliers final: 56 residues processed: 282 average time/residue: 0.3292 time to fit residues: 148.6982 Evaluate side-chains 265 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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 295 LEU 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 794 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 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 1082 VAL Chi-restraints excluded: chain A residue 1129 LEU 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 351 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 496 MET 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 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 81 LEU Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 479 MET Chi-restraints excluded: chain F residue 509 PHE Chi-restraints excluded: chain F residue 557 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 207 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** D 716 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.224676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.178889 restraints weight = 34524.674| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 2.89 r_work: 0.4084 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2073 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= 0.124 Angle : 0.571 17.315 30987 Z= 0.282 Chirality : 0.041 0.187 3491 Planarity : 0.004 0.049 3929 Dihedral : 4.086 31.007 3027 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.32 % Allowed : 15.81 % Favored : 80.87 % 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: 0.34 (0.16), residues: 2791 helix: 1.78 (0.15), residues: 1211 sheet: -0.72 (0.23), residues: 527 loop : -1.08 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 406 HIS 0.004 0.001 HIS D 729 PHE 0.013 0.001 PHE F 254 TYR 0.016 0.001 TYR A 235 ARG 0.003 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 996) hydrogen bonds : angle 4.23625 ( 2880) covalent geometry : bond 0.00284 (22878) covalent geometry : angle 0.57147 (30987) *********************** 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 297 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 215 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6682 (t80) REVERT: A 324 MET cc_start: 0.6480 (mmm) cc_final: 0.6135 (mpp) REVERT: A 406 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7703 (mt) REVERT: A 540 TRP cc_start: 0.6874 (m100) cc_final: 0.6001 (m100) REVERT: A 920 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7741 (p) REVERT: A 1044 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8011 (pp) REVERT: A 1143 CYS cc_start: 0.7777 (m) cc_final: 0.7325 (m) REVERT: B 60 ASP cc_start: 0.6773 (t0) cc_final: 0.6533 (t0) REVERT: C 161 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: C 254 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5116 (m-80) REVERT: C 303 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6953 (m) REVERT: C 463 ILE cc_start: 0.8244 (mp) cc_final: 0.7902 (mp) REVERT: C 542 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6944 (mmm) REVERT: D 534 MET cc_start: 0.3990 (tmm) cc_final: 0.2950 (ptm) REVERT: D 659 LEU cc_start: 0.2405 (OUTLIER) cc_final: 0.1909 (pp) REVERT: E 81 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8501 (tt) REVERT: F 254 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.4632 (t80) REVERT: F 406 TRP cc_start: 0.5712 (m-90) cc_final: 0.5369 (m-90) REVERT: F 509 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5125 (t80) REVERT: F 514 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6043 (mt0) outliers start: 82 outliers final: 52 residues processed: 271 average time/residue: 0.3261 time to fit residues: 142.5784 Evaluate side-chains 271 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 295 LEU 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 417 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE 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 1079 ASP Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 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 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 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 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 303 THR 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 519 VAL 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: 0.9990 chunk 66 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 146 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A 880 HIS ** D 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.224425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4415 r_free = 0.4415 target = 0.172492 restraints weight = 35136.029| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 3.75 r_work: 0.4060 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2204 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= 0.124 Angle : 0.578 15.487 30987 Z= 0.284 Chirality : 0.041 0.246 3491 Planarity : 0.004 0.052 3929 Dihedral : 4.052 29.195 3027 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.40 % Allowed : 16.42 % Favored : 80.19 % 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: 0.36 (0.16), residues: 2791 helix: 1.81 (0.15), residues: 1213 sheet: -0.79 (0.23), residues: 537 loop : -1.04 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 406 HIS 0.006 0.001 HIS D 729 PHE 0.015 0.001 PHE A 707 TYR 0.015 0.001 TYR A 70 ARG 0.006 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 996) hydrogen bonds : angle 4.19701 ( 2880) covalent geometry : bond 0.00286 (22878) covalent geometry : angle 0.57810 (30987) *********************** 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 297 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6606 (t80) REVERT: A 240 MET cc_start: 0.4651 (ptt) cc_final: 0.3806 (ppp) REVERT: A 324 MET cc_start: 0.6514 (mmm) cc_final: 0.6296 (mpp) REVERT: A 406 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7673 (mt) REVERT: A 430 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7226 (mmm160) REVERT: A 540 TRP cc_start: 0.6818 (m100) cc_final: 0.5931 (m100) REVERT: A 920 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7593 (p) REVERT: A 1044 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7974 (pp) REVERT: A 1143 CYS cc_start: 0.7809 (m) cc_final: 0.7301 (m) REVERT: B 60 ASP cc_start: 0.6844 (t0) cc_final: 0.6611 (t0) REVERT: B 121 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6904 (ptm160) REVERT: C 161 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 254 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5061 (m-80) REVERT: C 463 ILE cc_start: 0.8265 (mp) cc_final: 0.7931 (mp) REVERT: C 542 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7036 (mmm) REVERT: D 534 MET cc_start: 0.3669 (tmm) cc_final: 0.2983 (ptm) REVERT: D 659 LEU cc_start: 0.2146 (OUTLIER) cc_final: 0.1757 (pp) REVERT: D 686 ASP cc_start: 0.7010 (t0) cc_final: 0.6675 (t0) REVERT: D 1017 MET cc_start: 0.7564 (mpp) cc_final: 0.7020 (mpp) REVERT: E 67 ARG cc_start: 0.6458 (ttm110) cc_final: 0.6256 (ttt180) REVERT: F 254 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.4668 (t80) REVERT: F 464 MET cc_start: 0.6341 (pmm) cc_final: 0.5446 (pmm) REVERT: F 509 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5062 (t80) REVERT: F 514 GLN cc_start: 0.6761 (mm-40) cc_final: 0.6126 (mt0) outliers start: 84 outliers final: 55 residues processed: 271 average time/residue: 0.3253 time to fit residues: 141.0506 Evaluate side-chains 273 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 849 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 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 1079 ASP Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1129 LEU 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 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 351 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 566 SER 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 947 LEU Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 364 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 46 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.223132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.173891 restraints weight = 34735.646| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 3.03 r_work: 0.4057 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22878 Z= 0.155 Angle : 0.612 15.547 30987 Z= 0.302 Chirality : 0.042 0.230 3491 Planarity : 0.004 0.056 3929 Dihedral : 4.230 30.554 3027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.80 % Allowed : 16.46 % Favored : 79.74 % 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: 1.69 (0.15), residues: 1211 sheet: -0.94 (0.23), residues: 537 loop : -1.13 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 406 HIS 0.005 0.001 HIS D 729 PHE 0.015 0.002 PHE F 395 TYR 0.018 0.002 TYR A 70 ARG 0.008 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 996) hydrogen bonds : angle 4.32443 ( 2880) covalent geometry : bond 0.00362 (22878) covalent geometry : angle 0.61247 (30987) *********************** 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 308 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 214 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6243 (t80) REVERT: A 240 MET cc_start: 0.4758 (ptt) cc_final: 0.3864 (ppp) REVERT: A 324 MET cc_start: 0.6429 (mmm) cc_final: 0.6178 (mpp) REVERT: A 406 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 430 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7022 (mmm160) REVERT: A 540 TRP cc_start: 0.6912 (m100) cc_final: 0.6576 (m100) REVERT: A 647 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7470 (ptm-80) REVERT: A 695 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: A 920 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7719 (p) REVERT: A 1044 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7942 (pp) REVERT: A 1143 CYS cc_start: 0.7814 (m) cc_final: 0.7478 (m) REVERT: B 121 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6977 (ptm160) REVERT: C 161 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: C 254 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: C 303 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6916 (m) REVERT: C 463 ILE cc_start: 0.8285 (mp) cc_final: 0.7945 (mp) REVERT: C 542 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6985 (mmm) REVERT: D 534 MET cc_start: 0.4166 (tmm) cc_final: 0.3099 (ptm) REVERT: D 659 LEU cc_start: 0.2283 (OUTLIER) cc_final: 0.1873 (pp) REVERT: D 686 ASP cc_start: 0.6994 (t0) cc_final: 0.6662 (t0) REVERT: E 91 LEU cc_start: 0.4160 (mm) cc_final: 0.3786 (mt) REVERT: F 254 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.4742 (t80) REVERT: F 464 MET cc_start: 0.6325 (pmm) cc_final: 0.5646 (pmm) REVERT: F 509 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5120 (t80) REVERT: F 514 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6083 (mt0) outliers start: 94 outliers final: 68 residues processed: 283 average time/residue: 0.3238 time to fit residues: 146.2866 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 : 2.503 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 502 HIS 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 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 690 CYS 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 849 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 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 1129 LEU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1187 TRP Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 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 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 359 PHE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 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 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 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 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: 0.6980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4901 r_free = 0.4901 target = 0.224024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.172940 restraints weight = 34586.486| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 3.47 r_work: 0.4063 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22878 Z= 0.124 Angle : 0.593 14.858 30987 Z= 0.291 Chirality : 0.041 0.231 3491 Planarity : 0.004 0.059 3929 Dihedral : 4.127 24.849 3027 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.44 % Allowed : 17.19 % Favored : 79.38 % 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: 0.25 (0.16), residues: 2791 helix: 1.75 (0.15), residues: 1213 sheet: -0.87 (0.23), residues: 513 loop : -1.14 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 340 HIS 0.005 0.001 HIS D 729 PHE 0.013 0.001 PHE F 254 TYR 0.018 0.001 TYR A 309 ARG 0.013 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 996) hydrogen bonds : angle 4.21131 ( 2880) covalent geometry : bond 0.00286 (22878) covalent geometry : angle 0.59319 (30987) *********************** 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: 85 poor density : 210 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6095 (t80) REVERT: A 240 MET cc_start: 0.4798 (ptt) cc_final: 0.3919 (ppp) REVERT: A 324 MET cc_start: 0.6406 (mmm) cc_final: 0.6156 (mpp) REVERT: A 406 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7649 (mt) REVERT: A 430 ARG cc_start: 0.7649 (mmm160) cc_final: 0.7047 (mmm160) REVERT: A 540 TRP cc_start: 0.6845 (m100) cc_final: 0.6517 (m100) REVERT: A 695 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: A 920 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7548 (p) REVERT: A 1044 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7970 (pp) REVERT: A 1131 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: A 1143 CYS cc_start: 0.7818 (m) cc_final: 0.7474 (m) REVERT: B 60 ASP cc_start: 0.6798 (t0) cc_final: 0.6560 (t0) REVERT: C 161 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: C 254 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5071 (m-80) REVERT: C 303 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6931 (m) REVERT: C 344 SER cc_start: 0.8466 (m) cc_final: 0.8246 (t) REVERT: C 463 ILE cc_start: 0.8272 (mp) cc_final: 0.7928 (mp) REVERT: C 542 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7036 (mmm) REVERT: D 87 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6555 (pptt) REVERT: D 534 MET cc_start: 0.4519 (tmm) cc_final: 0.3529 (ptm) REVERT: D 659 LEU cc_start: 0.2281 (OUTLIER) cc_final: 0.1849 (pp) REVERT: D 686 ASP cc_start: 0.6992 (t0) cc_final: 0.6659 (t0) REVERT: E 58 LEU cc_start: 0.4077 (tt) cc_final: 0.3534 (tp) REVERT: E 91 LEU cc_start: 0.4109 (mm) cc_final: 0.3848 (pp) REVERT: F 254 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.4736 (t80) REVERT: F 464 MET cc_start: 0.6555 (pmm) cc_final: 0.5774 (pmm) REVERT: F 509 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.5070 (t80) REVERT: F 514 GLN cc_start: 0.6746 (mm-40) cc_final: 0.6175 (mt0) outliers start: 85 outliers final: 66 residues processed: 273 average time/residue: 0.3221 time to fit residues: 141.4665 Evaluate side-chains 283 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 204 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 861 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 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 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 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 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 359 PHE 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 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 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 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: 0.9990 chunk 172 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 250 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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 = 0.4902 r_free = 0.4902 target = 0.224486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.4424 r_free = 0.4424 target = 0.174898 restraints weight = 34671.809| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 4.05 r_work: 0.4054 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22878 Z= 0.125 Angle : 0.593 14.504 30987 Z= 0.293 Chirality : 0.041 0.218 3491 Planarity : 0.004 0.060 3929 Dihedral : 4.112 24.524 3027 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.48 % Allowed : 16.98 % Favored : 79.54 % 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: 0.26 (0.16), residues: 2791 helix: 1.74 (0.15), residues: 1213 sheet: -0.83 (0.23), residues: 503 loop : -1.13 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 406 HIS 0.005 0.001 HIS D 729 PHE 0.025 0.001 PHE D 99 TYR 0.017 0.001 TYR A 883 ARG 0.008 0.000 ARG A 647 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 996) hydrogen bonds : angle 4.18652 ( 2880) covalent geometry : bond 0.00286 (22878) covalent geometry : angle 0.59333 (30987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 207 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6052 (t80) REVERT: A 240 MET cc_start: 0.4859 (ptt) cc_final: 0.3893 (ppp) REVERT: A 324 MET cc_start: 0.6470 (mmm) cc_final: 0.6216 (mpp) REVERT: A 406 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7649 (mt) REVERT: A 430 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7127 (mmm160) REVERT: A 695 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: A 920 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7530 (p) REVERT: A 1044 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7988 (pp) REVERT: A 1131 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: A 1143 CYS cc_start: 0.7862 (m) cc_final: 0.7504 (m) REVERT: B 60 ASP cc_start: 0.6583 (t0) cc_final: 0.6342 (t0) REVERT: C 161 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: C 254 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5072 (m-80) REVERT: C 303 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6948 (m) REVERT: C 463 ILE cc_start: 0.8273 (mp) cc_final: 0.7893 (mp) REVERT: C 464 MET cc_start: 0.7980 (mmp) cc_final: 0.7747 (mmm) REVERT: C 542 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7068 (mmm) REVERT: D 87 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6554 (pptt) REVERT: D 534 MET cc_start: 0.4489 (tmm) cc_final: 0.3527 (ptm) REVERT: D 659 LEU cc_start: 0.2271 (OUTLIER) cc_final: 0.1855 (pp) REVERT: D 686 ASP cc_start: 0.6986 (t0) cc_final: 0.6650 (t0) REVERT: E 58 LEU cc_start: 0.4157 (tt) cc_final: 0.3605 (tp) REVERT: E 91 LEU cc_start: 0.4265 (mm) cc_final: 0.3955 (pp) REVERT: F 254 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.4758 (t80) REVERT: F 464 MET cc_start: 0.6546 (pmm) cc_final: 0.5780 (pmm) REVERT: F 509 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5060 (t80) REVERT: F 514 GLN cc_start: 0.6736 (mm-40) cc_final: 0.6176 (mt0) outliers start: 86 outliers final: 66 residues processed: 272 average time/residue: 0.3401 time to fit residues: 148.7461 Evaluate side-chains 281 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 502 HIS 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 695 GLN Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 849 LEU 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 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 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 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 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 359 PHE 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 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 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: 0.0010 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 86 optimal weight: 0.0030 chunk 142 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.225156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.179849 restraints weight = 34182.904| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.58 r_work: 0.4109 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22878 Z= 0.115 Angle : 0.592 14.331 30987 Z= 0.289 Chirality : 0.041 0.214 3491 Planarity : 0.004 0.058 3929 Dihedral : 4.042 23.734 3027 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.36 % Allowed : 17.31 % 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: 0.34 (0.16), residues: 2791 helix: 1.78 (0.15), residues: 1213 sheet: -0.73 (0.23), residues: 503 loop : -1.08 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 406 HIS 0.005 0.001 HIS D 729 PHE 0.030 0.001 PHE D 99 TYR 0.018 0.001 TYR A 883 ARG 0.009 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 996) hydrogen bonds : angle 4.16003 ( 2880) covalent geometry : bond 0.00261 (22878) covalent geometry : angle 0.59200 (30987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15019.77 seconds wall clock time: 262 minutes 32.21 seconds (15752.21 seconds total)