Starting phenix.real_space_refine on Sat Jan 18 23:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmq_38486/01_2025/8xmq_38486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmq_38486/01_2025/8xmq_38486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmq_38486/01_2025/8xmq_38486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmq_38486/01_2025/8xmq_38486.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmq_38486/01_2025/8xmq_38486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmq_38486/01_2025/8xmq_38486_neut.cif" } resolution = 3.21 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 Fe 2 7.16 5 S 108 5.16 5 C 8074 2.51 5 N 2277 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12950 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2117 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 13, 'TRANS': 256} Chain breaks: 2 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3367 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 4, 'TRANS': 435} Chain breaks: 2 Chain: "D" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5066 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 19, 'TRANS': 644} Chain breaks: 7 Chain: "C" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1057 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {' CA': 6, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 34 Unusual residues: {' CA': 6, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.19, per 1000 atoms: 0.63 Number of scatterers: 12950 At special positions: 0 Unit cell: (89.88, 127.33, 172.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 12 19.99 S 108 16.00 O 2477 8.00 N 2277 7.00 C 8074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 258 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS F 275 " - pdb=" SG CYS F 309 " distance=2.04 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 365 " distance=2.03 Simple disulfide: pdb=" SG CYS F 335 " - pdb=" SG CYS F 345 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 472 " distance=2.03 Simple disulfide: pdb=" SG CYS F 442 " - pdb=" SG CYS F 452 " distance=2.04 Simple disulfide: pdb=" SG CYS F 728 " - pdb=" SG CYS F 762 " distance=2.03 Simple disulfide: pdb=" SG CYS F 744 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 757 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03 Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.03 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.03 Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.02 Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.03 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG A 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG D1102 " - " ASN D1027 " " NAG F1107 " - " ASN F 320 " " NAG F1108 " - " ASN F 445 " " NAG F1109 " - " ASN F 767 " " NAG Y 1 " - " ASN D 320 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 27 sheets defined 28.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 157 through 162 removed outlier: 3.923A pdb=" N THR 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 333 through 344 removed outlier: 4.797A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.814A pdb=" N ASP F 253 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 403 through 415 removed outlier: 3.600A pdb=" N ALA F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.604A pdb=" N ASP F 813 " --> pdb=" O HIS F 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.516A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 504 through 507 removed outlier: 4.106A pdb=" N PHE D 507 " --> pdb=" O ASP D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 613 through 620 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 856 through 868 Processing helix chain 'D' and resid 901 through 905 removed outlier: 3.520A pdb=" N GLN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 971 Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.641A pdb=" N ASP D1023 " --> pdb=" O HIS D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.720A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.670A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.924A pdb=" N LYS G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 4.242A pdb=" N GLY G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 43 removed outlier: 3.593A pdb=" N PHE G 41 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 57 through 77 Processing helix chain 'G' and resid 80 through 85 removed outlier: 3.910A pdb=" N THR G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 95 Processing helix chain 'G' and resid 99 through 119 removed outlier: 3.931A pdb=" N PHE G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.024A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.626A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.759A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.759A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 279 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE F 290 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TRP F 287 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU F 330 " --> pdb=" O TRP F 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR F 289 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 371 through 377 removed outlier: 3.866A pdb=" N LYS F 421 " --> pdb=" O THR F 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 396 through 397 removed outlier: 6.932A pdb=" N LYS F 396 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU F 439 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 720 through 722 Processing sheet with id=AB2, first strand: chain 'F' and resid 720 through 722 removed outlier: 14.930A pdb=" N GLY F 730 " --> pdb=" O ASP F 745 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ASP F 745 " --> pdb=" O GLY F 730 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL F 732 " --> pdb=" O ILE F 743 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE F 743 " --> pdb=" O VAL F 732 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU F 783 " --> pdb=" O THR F 742 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU F 785 " --> pdb=" O CYS F 744 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP F 746 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 823 through 824 Processing sheet with id=AB4, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AB5, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.656A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.656A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS D 327 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 371 through 380 removed outlier: 3.511A pdb=" N GLY D 378 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR D 471 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 371 through 380 removed outlier: 3.511A pdb=" N GLY D 378 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.223A pdb=" N GLY D 574 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 527 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 576 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.139A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TRP D 499 " --> pdb=" O GLN D 539 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AC4, first strand: chain 'D' and resid 597 through 600 Processing sheet with id=AC5, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AC6, first strand: chain 'D' and resid 836 through 838 removed outlier: 3.852A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 840 through 843 removed outlier: 6.352A pdb=" N TRP D 889 " --> pdb=" O TRP D 847 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D 849 " --> pdb=" O TRP D 889 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.311A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TRP D 992 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR D 952 " --> pdb=" O TRP D 992 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 929 through 932 507 hydrogen bonds defined for protein. 1386 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: 5.16 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5375 1.39 - 1.56: 7742 1.56 - 1.72: 0 1.72 - 1.89: 125 1.89 - 2.05: 8 Bond restraints: 13250 Sorted by residual: bond pdb=" N GLU D 920 " pdb=" CA GLU D 920 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.20e-02 6.94e+03 5.38e+00 bond pdb=" N VAL 2 271 " pdb=" CA VAL 2 271 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.58e+00 bond pdb=" N THR D 921 " pdb=" CA THR D 921 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.30e-02 5.92e+03 4.34e+00 bond pdb=" N ILE 2 344 " pdb=" CA ILE 2 344 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.25e-02 6.40e+03 3.74e+00 bond pdb=" C VAL 2 269 " pdb=" N GLY 2 270 " ideal model delta sigma weight residual 1.331 1.302 0.028 1.46e-02 4.69e+03 3.68e+00 ... (remaining 13245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17429 1.38 - 2.76: 432 2.76 - 4.14: 93 4.14 - 5.52: 16 5.52 - 6.90: 7 Bond angle restraints: 17977 Sorted by residual: angle pdb=" C THR D 921 " pdb=" CA THR D 921 " pdb=" CB THR D 921 " ideal model delta sigma weight residual 111.83 104.93 6.90 1.60e+00 3.91e-01 1.86e+01 angle pdb=" N ALA 2 345 " pdb=" CA ALA 2 345 " pdb=" C ALA 2 345 " ideal model delta sigma weight residual 111.71 106.94 4.77 1.34e+00 5.57e-01 1.27e+01 angle pdb=" O VAL 2 269 " pdb=" C VAL 2 269 " pdb=" N GLY 2 270 " ideal model delta sigma weight residual 122.69 118.75 3.94 1.14e+00 7.69e-01 1.20e+01 angle pdb=" CA THR D 921 " pdb=" C THR D 921 " pdb=" O THR D 921 " ideal model delta sigma weight residual 122.41 118.40 4.01 1.21e+00 6.83e-01 1.10e+01 angle pdb=" C VAL 2 269 " pdb=" N GLY 2 270 " pdb=" CA GLY 2 270 " ideal model delta sigma weight residual 121.41 114.93 6.48 1.96e+00 2.60e-01 1.09e+01 ... (remaining 17972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7115 17.93 - 35.86: 639 35.86 - 53.80: 115 53.80 - 71.73: 25 71.73 - 89.66: 11 Dihedral angle restraints: 7905 sinusoidal: 3272 harmonic: 4633 Sorted by residual: dihedral pdb=" CB CYS F 275 " pdb=" SG CYS F 275 " pdb=" SG CYS F 309 " pdb=" CB CYS F 309 " ideal model delta sinusoidal sigma weight residual 93.00 179.91 -86.91 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual -86.00 -144.09 58.09 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CB CYS 2 90 " pdb=" SG CYS 2 90 " pdb=" SG CYS 2 207 " pdb=" CB CYS 2 207 " ideal model delta sinusoidal sigma weight residual 93.00 35.31 57.69 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 7902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1262 0.036 - 0.072: 475 0.072 - 0.108: 158 0.108 - 0.144: 35 0.144 - 0.180: 3 Chirality restraints: 1933 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN D 320 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ILE 2 344 " pdb=" N ILE 2 344 " pdb=" C ILE 2 344 " pdb=" CB ILE 2 344 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA PRO D 310 " pdb=" N PRO D 310 " pdb=" C PRO D 310 " pdb=" CB PRO D 310 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1930 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR 2 343 " -0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C THR 2 343 " 0.072 2.00e-02 2.50e+03 pdb=" O THR 2 343 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE 2 344 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 2 269 " -0.011 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C VAL 2 269 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL 2 269 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY 2 270 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 124 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO G 125 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 210 2.64 - 3.20: 11619 3.20 - 3.77: 20918 3.77 - 4.33: 29302 4.33 - 4.90: 48073 Nonbonded interactions: 110122 Sorted by model distance: nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.074 3.040 nonbonded pdb=" OG SER D 366 " pdb=" OD1 ASP D 370 " model vdw 2.184 3.040 nonbonded pdb=" NH1 ARG C 31 " pdb=" OE1 GLN G 127 " model vdw 2.186 3.120 nonbonded pdb=" O ILE D 328 " pdb=" NE2 HIS D 353 " model vdw 2.200 3.120 nonbonded pdb=" OE1 GLU D 359 " pdb="CA CA D1103 " model vdw 2.229 2.510 ... (remaining 110117 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 'Y' } 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=0.52 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 32.610 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13250 Z= 0.237 Angle : 0.558 6.899 17977 Z= 0.304 Chirality : 0.043 0.180 1933 Planarity : 0.003 0.043 2309 Dihedral : 13.774 89.662 4813 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 0.15 % Allowed : 0.37 % Favored : 99.48 % 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: -0.24 (0.21), residues: 1625 helix: 1.85 (0.28), residues: 377 sheet: -0.56 (0.41), residues: 180 loop : -0.86 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 992 HIS 0.010 0.001 HIS C 122 PHE 0.010 0.001 PHE G 71 TYR 0.008 0.001 TYR 2 221 ARG 0.002 0.000 ARG 2 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8563 (m) cc_final: 0.8046 (t) REVERT: 2 202 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7016 (mtp85) REVERT: 2 232 LYS cc_start: 0.8534 (tptt) cc_final: 0.8320 (ttpp) REVERT: 2 286 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7814 (ttpp) REVERT: F 187 ASN cc_start: 0.7765 (t0) cc_final: 0.7506 (t0) REVERT: F 269 VAL cc_start: 0.7895 (p) cc_final: 0.7653 (m) REVERT: F 822 MET cc_start: 0.6572 (mtm) cc_final: 0.5961 (ttp) REVERT: D 840 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6282 (pt0) REVERT: D 874 LYS cc_start: 0.7965 (mttm) cc_final: 0.7657 (pttp) REVERT: D 919 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.3954 (pt0) REVERT: D 960 LEU cc_start: 0.7961 (tp) cc_final: 0.7571 (tt) REVERT: C 56 LYS cc_start: 0.7132 (tttt) cc_final: 0.6556 (mmmt) REVERT: C 90 LYS cc_start: 0.7988 (tttp) cc_final: 0.7515 (mtpt) REVERT: C 127 LYS cc_start: 0.8659 (mttp) cc_final: 0.8280 (mtmt) REVERT: G 95 LYS cc_start: 0.8384 (mppt) cc_final: 0.8161 (ttpt) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.2900 time to fit residues: 131.5238 Evaluate side-chains 185 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 272 GLN Chi-restraints excluded: chain D residue 919 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 341 GLN F 189 ASN F 327 HIS F 759 GLN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 801 HIS F 810 HIS D 431 GLN D 539 GLN D 622 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.179332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141478 restraints weight = 15321.369| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.70 r_work: 0.3140 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13250 Z= 0.376 Angle : 0.623 8.686 17977 Z= 0.321 Chirality : 0.046 0.183 1933 Planarity : 0.004 0.058 2309 Dihedral : 6.769 79.659 1989 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 2.36 % Allowed : 10.10 % Favored : 87.55 % 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: -0.56 (0.20), residues: 1625 helix: 1.62 (0.27), residues: 376 sheet: -1.25 (0.35), residues: 194 loop : -0.97 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 847 HIS 0.011 0.001 HIS C 122 PHE 0.019 0.002 PHE D 842 TYR 0.018 0.002 TYR C 140 ARG 0.008 0.001 ARG D 562 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.495 Fit side-chains REVERT: 2 198 SER cc_start: 0.8666 (m) cc_final: 0.8377 (t) REVERT: 2 202 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7425 (mtp85) REVERT: F 187 ASN cc_start: 0.8001 (t0) cc_final: 0.7394 (t0) REVERT: F 283 PHE cc_start: 0.7444 (t80) cc_final: 0.7152 (t80) REVERT: F 447 THR cc_start: 0.8575 (t) cc_final: 0.8297 (p) REVERT: F 847 TRP cc_start: 0.7074 (m100) cc_final: 0.6795 (m100) REVERT: D 399 ASP cc_start: 0.9000 (p0) cc_final: 0.8759 (p0) REVERT: D 874 LYS cc_start: 0.7948 (mttm) cc_final: 0.7438 (pttp) REVERT: D 960 LEU cc_start: 0.7943 (tp) cc_final: 0.7532 (tt) REVERT: D 994 ASN cc_start: 0.7462 (p0) cc_final: 0.6890 (p0) REVERT: D 1012 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8148 (mtp85) REVERT: C 50 HIS cc_start: 0.8748 (t70) cc_final: 0.8521 (t-90) REVERT: C 56 LYS cc_start: 0.7939 (tttt) cc_final: 0.7407 (mmmt) REVERT: C 90 LYS cc_start: 0.8246 (tttp) cc_final: 0.7946 (mtpt) REVERT: G 95 LYS cc_start: 0.8669 (mppt) cc_final: 0.8227 (ttpt) outliers start: 32 outliers final: 18 residues processed: 213 average time/residue: 0.2941 time to fit residues: 88.8498 Evaluate side-chains 183 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 204 MET Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 787 LYS Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 0.0050 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 240 HIS F 327 HIS F 797 GLN D 456 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141522 restraints weight = 15482.184| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.70 r_work: 0.3144 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13250 Z= 0.274 Angle : 0.544 6.888 17977 Z= 0.282 Chirality : 0.043 0.154 1933 Planarity : 0.004 0.041 2309 Dihedral : 6.095 84.784 1983 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 2.21 % Allowed : 12.97 % Favored : 84.82 % 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 (0.20), residues: 1625 helix: 1.76 (0.27), residues: 378 sheet: -1.62 (0.34), residues: 179 loop : -0.98 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D1013 HIS 0.011 0.001 HIS F 240 PHE 0.017 0.001 PHE D 842 TYR 0.015 0.002 TYR D 465 ARG 0.004 0.000 ARG D1012 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8636 (m) cc_final: 0.8413 (t) REVERT: 2 202 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7420 (mtp85) REVERT: 2 272 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8335 (tp40) REVERT: F 187 ASN cc_start: 0.7916 (t0) cc_final: 0.7270 (t0) REVERT: F 245 LYS cc_start: 0.8010 (tttt) cc_final: 0.7659 (tmtt) REVERT: F 283 PHE cc_start: 0.7639 (t80) cc_final: 0.7282 (t80) REVERT: F 447 THR cc_start: 0.8533 (t) cc_final: 0.8282 (p) REVERT: F 822 MET cc_start: 0.7352 (mtt) cc_final: 0.5882 (ttp) REVERT: D 543 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8123 (mt-10) REVERT: D 874 LYS cc_start: 0.7969 (mttm) cc_final: 0.7489 (pttp) REVERT: D 960 LEU cc_start: 0.7970 (tp) cc_final: 0.7470 (tt) REVERT: D 1012 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8187 (mtp85) REVERT: C 56 LYS cc_start: 0.7893 (tttt) cc_final: 0.7377 (mmmt) REVERT: G 95 LYS cc_start: 0.8657 (mppt) cc_final: 0.8265 (ttpt) outliers start: 30 outliers final: 21 residues processed: 197 average time/residue: 0.2586 time to fit residues: 74.3917 Evaluate side-chains 177 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 272 GLN Chi-restraints excluded: chain 2 residue 284 MET Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 787 LYS Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 0.0060 chunk 123 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 272 GLN F 240 HIS F 327 HIS G 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.175872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137687 restraints weight = 15245.132| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.67 r_work: 0.3100 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13250 Z= 0.375 Angle : 0.593 8.247 17977 Z= 0.303 Chirality : 0.045 0.170 1933 Planarity : 0.004 0.042 2309 Dihedral : 6.070 87.476 1983 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 3.10 % Allowed : 14.66 % Favored : 82.24 % 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: -0.72 (0.20), residues: 1625 helix: 1.52 (0.27), residues: 379 sheet: -1.71 (0.33), residues: 199 loop : -1.02 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D1013 HIS 0.012 0.001 HIS F 240 PHE 0.019 0.002 PHE D 842 TYR 0.015 0.002 TYR 2 239 ARG 0.003 0.000 ARG F 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8702 (m) cc_final: 0.8493 (t) REVERT: 2 202 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7434 (mtp85) REVERT: F 187 ASN cc_start: 0.7987 (t0) cc_final: 0.7231 (t0) REVERT: F 245 LYS cc_start: 0.8109 (tttt) cc_final: 0.7788 (tmtt) REVERT: F 283 PHE cc_start: 0.7683 (t80) cc_final: 0.7169 (t80) REVERT: F 447 THR cc_start: 0.8541 (t) cc_final: 0.8284 (p) REVERT: F 822 MET cc_start: 0.7456 (mtt) cc_final: 0.5843 (ttp) REVERT: F 847 TRP cc_start: 0.7393 (m100) cc_final: 0.7118 (m100) REVERT: D 344 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: D 400 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7907 (ttm110) REVERT: D 543 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8274 (mt-10) REVERT: D 874 LYS cc_start: 0.8028 (mttm) cc_final: 0.7440 (pttp) REVERT: D 960 LEU cc_start: 0.7937 (tp) cc_final: 0.7394 (tt) REVERT: C 56 LYS cc_start: 0.7920 (tttt) cc_final: 0.7408 (mmmt) REVERT: G 95 LYS cc_start: 0.8661 (mppt) cc_final: 0.8261 (ttpt) outliers start: 42 outliers final: 29 residues processed: 187 average time/residue: 0.2615 time to fit residues: 70.8019 Evaluate side-chains 184 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 271 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.0980 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 327 HIS F 338 HIS C 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.179218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128201 restraints weight = 15729.482| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.26 r_work: 0.3256 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13250 Z= 0.236 Angle : 0.529 7.158 17977 Z= 0.273 Chirality : 0.042 0.153 1933 Planarity : 0.004 0.049 2309 Dihedral : 5.765 89.007 1983 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.73 % Allowed : 16.06 % Favored : 81.21 % 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: -0.51 (0.20), residues: 1625 helix: 1.87 (0.27), residues: 377 sheet: -1.66 (0.35), residues: 186 loop : -0.95 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D1013 HIS 0.006 0.001 HIS C 122 PHE 0.016 0.001 PHE D 842 TYR 0.012 0.001 TYR 2 239 ARG 0.005 0.000 ARG D1011 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.485 Fit side-chains REVERT: 2 198 SER cc_start: 0.8750 (m) cc_final: 0.8498 (t) REVERT: 2 202 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7146 (mtp85) REVERT: F 187 ASN cc_start: 0.7753 (t0) cc_final: 0.7414 (t0) REVERT: F 200 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5595 (mp) REVERT: F 245 LYS cc_start: 0.8158 (tttt) cc_final: 0.7813 (tmtt) REVERT: F 447 THR cc_start: 0.8593 (t) cc_final: 0.8267 (p) REVERT: F 822 MET cc_start: 0.7335 (mtt) cc_final: 0.5624 (ttp) REVERT: F 847 TRP cc_start: 0.7211 (m100) cc_final: 0.6869 (m100) REVERT: D 344 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: D 400 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7740 (ttm110) REVERT: D 435 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7416 (m) REVERT: D 543 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 874 LYS cc_start: 0.7999 (mttm) cc_final: 0.7300 (pttp) REVERT: D 932 GLN cc_start: 0.8164 (mt0) cc_final: 0.7877 (mt0) REVERT: C 56 LYS cc_start: 0.7596 (tttt) cc_final: 0.7012 (mmmt) REVERT: G 95 LYS cc_start: 0.8651 (mppt) cc_final: 0.8092 (ttpt) outliers start: 37 outliers final: 29 residues processed: 187 average time/residue: 0.2484 time to fit residues: 69.0932 Evaluate side-chains 184 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 284 MET Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 240 HIS F 327 HIS F 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.178495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121028 restraints weight = 15910.688| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.26 r_work: 0.3231 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13250 Z= 0.296 Angle : 0.550 7.442 17977 Z= 0.283 Chirality : 0.044 0.169 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.781 87.025 1983 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 16.29 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.20), residues: 1625 helix: 1.77 (0.27), residues: 378 sheet: -1.83 (0.36), residues: 170 loop : -0.93 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D1013 HIS 0.011 0.001 HIS F 240 PHE 0.024 0.001 PHE F 283 TYR 0.014 0.001 TYR 2 239 ARG 0.005 0.000 ARG D1012 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.333 Fit side-chains REVERT: 2 198 SER cc_start: 0.8756 (m) cc_final: 0.8516 (t) REVERT: 2 202 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7252 (mtp85) REVERT: F 187 ASN cc_start: 0.7773 (t0) cc_final: 0.7402 (t0) REVERT: F 245 LYS cc_start: 0.8152 (tttt) cc_final: 0.7759 (tmtt) REVERT: F 447 THR cc_start: 0.8480 (t) cc_final: 0.8192 (p) REVERT: F 822 MET cc_start: 0.7365 (mtt) cc_final: 0.5695 (ttp) REVERT: F 847 TRP cc_start: 0.7288 (m100) cc_final: 0.6793 (m100) REVERT: D 344 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: D 400 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7760 (ttm110) REVERT: D 435 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.7965 (t) REVERT: D 543 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8011 (mt-10) REVERT: D 874 LYS cc_start: 0.8023 (mttm) cc_final: 0.7248 (pttp) REVERT: D 932 GLN cc_start: 0.8241 (mt0) cc_final: 0.7943 (mt0) REVERT: D 1012 ARG cc_start: 0.8780 (ptm160) cc_final: 0.7370 (ptm160) REVERT: D 1013 TRP cc_start: 0.6282 (m-90) cc_final: 0.6077 (m-90) REVERT: C 56 LYS cc_start: 0.7605 (tttt) cc_final: 0.7002 (mmmt) REVERT: C 90 LYS cc_start: 0.8416 (tttp) cc_final: 0.7948 (mtpt) REVERT: G 95 LYS cc_start: 0.8657 (mppt) cc_final: 0.8099 (ttpt) outliers start: 40 outliers final: 35 residues processed: 188 average time/residue: 0.2604 time to fit residues: 71.5432 Evaluate side-chains 190 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 271 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123144 restraints weight = 15802.835| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.43 r_work: 0.3246 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13250 Z= 0.265 Angle : 0.548 9.040 17977 Z= 0.283 Chirality : 0.043 0.197 1933 Planarity : 0.004 0.046 2309 Dihedral : 5.706 82.291 1983 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.87 % Allowed : 17.76 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.21), residues: 1625 helix: 1.89 (0.27), residues: 378 sheet: -1.79 (0.36), residues: 176 loop : -0.94 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1013 HIS 0.016 0.001 HIS F 240 PHE 0.020 0.001 PHE F 283 TYR 0.012 0.001 TYR 2 239 ARG 0.002 0.000 ARG D1012 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.398 Fit side-chains REVERT: 2 198 SER cc_start: 0.8756 (m) cc_final: 0.8504 (t) REVERT: 2 202 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7279 (mtp85) REVERT: F 187 ASN cc_start: 0.7789 (t0) cc_final: 0.7419 (t0) REVERT: F 245 LYS cc_start: 0.8197 (tttt) cc_final: 0.7785 (tmtt) REVERT: F 283 PHE cc_start: 0.6736 (t80) cc_final: 0.6149 (t80) REVERT: F 447 THR cc_start: 0.8453 (t) cc_final: 0.8177 (p) REVERT: F 822 MET cc_start: 0.7107 (mtt) cc_final: 0.5600 (ttp) REVERT: F 842 PHE cc_start: 0.6248 (t80) cc_final: 0.5768 (t80) REVERT: D 167 MET cc_start: 0.7985 (mtm) cc_final: 0.7727 (mtm) REVERT: D 344 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: D 400 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7671 (ttm110) REVERT: D 435 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.7957 (t) REVERT: D 543 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 874 LYS cc_start: 0.8054 (mttm) cc_final: 0.7312 (pttp) REVERT: D 932 GLN cc_start: 0.8082 (mt0) cc_final: 0.7812 (mt0) REVERT: D 1012 ARG cc_start: 0.8834 (ptm160) cc_final: 0.7552 (ptm160) REVERT: D 1013 TRP cc_start: 0.6297 (m-90) cc_final: 0.6032 (m-90) REVERT: C 56 LYS cc_start: 0.7575 (tttt) cc_final: 0.6992 (mmmt) REVERT: C 90 LYS cc_start: 0.8450 (tttp) cc_final: 0.7910 (mtpt) REVERT: G 95 LYS cc_start: 0.8651 (mppt) cc_final: 0.8089 (ttpt) outliers start: 39 outliers final: 32 residues processed: 183 average time/residue: 0.2611 time to fit residues: 69.1715 Evaluate side-chains 185 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 137 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122514 restraints weight = 15821.562| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.24 r_work: 0.3256 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13250 Z= 0.254 Angle : 0.535 7.542 17977 Z= 0.275 Chirality : 0.043 0.160 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.648 82.117 1983 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 2.87 % Allowed : 17.91 % Favored : 79.22 % 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: -0.46 (0.21), residues: 1625 helix: 1.97 (0.27), residues: 377 sheet: -1.83 (0.35), residues: 184 loop : -0.90 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP F 847 HIS 0.010 0.001 HIS F 240 PHE 0.019 0.001 PHE F 283 TYR 0.012 0.001 TYR 2 239 ARG 0.002 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.353 Fit side-chains REVERT: 2 198 SER cc_start: 0.8767 (m) cc_final: 0.8534 (t) REVERT: 2 202 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7303 (mtp85) REVERT: F 187 ASN cc_start: 0.7828 (t0) cc_final: 0.7442 (t0) REVERT: F 245 LYS cc_start: 0.8246 (tttt) cc_final: 0.7820 (tmtt) REVERT: F 447 THR cc_start: 0.8467 (t) cc_final: 0.8211 (p) REVERT: F 796 TRP cc_start: 0.6309 (p90) cc_final: 0.5946 (p-90) REVERT: F 822 MET cc_start: 0.7175 (mtt) cc_final: 0.5711 (ttp) REVERT: F 842 PHE cc_start: 0.6240 (t80) cc_final: 0.5894 (t80) REVERT: D 344 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: D 400 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7679 (ttm110) REVERT: D 435 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7950 (t) REVERT: D 543 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7915 (mt-10) REVERT: D 874 LYS cc_start: 0.8069 (mttm) cc_final: 0.7321 (pttp) REVERT: D 932 GLN cc_start: 0.8119 (mt0) cc_final: 0.7867 (mt0) REVERT: D 1012 ARG cc_start: 0.8840 (ptm160) cc_final: 0.7556 (ptm160) REVERT: D 1013 TRP cc_start: 0.6347 (m-90) cc_final: 0.6062 (m-90) REVERT: C 56 LYS cc_start: 0.7614 (tttt) cc_final: 0.7051 (mmmt) REVERT: C 90 LYS cc_start: 0.8530 (tttp) cc_final: 0.8001 (mtpt) REVERT: G 95 LYS cc_start: 0.8656 (mppt) cc_final: 0.8103 (ttpt) outliers start: 39 outliers final: 34 residues processed: 181 average time/residue: 0.2655 time to fit residues: 70.2819 Evaluate side-chains 186 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 266 LYS Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 144 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 0.2980 chunk 160 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.178111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126818 restraints weight = 15732.235| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.30 r_work: 0.3264 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13250 Z= 0.257 Angle : 0.546 11.513 17977 Z= 0.278 Chirality : 0.043 0.163 1933 Planarity : 0.004 0.044 2309 Dihedral : 5.647 81.949 1983 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 2.87 % Allowed : 17.98 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1625 helix: 1.94 (0.27), residues: 383 sheet: -1.77 (0.37), residues: 176 loop : -0.92 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP F 847 HIS 0.006 0.001 HIS F 327 PHE 0.016 0.001 PHE D 842 TYR 0.012 0.001 TYR 2 239 ARG 0.005 0.000 ARG F 825 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.414 Fit side-chains REVERT: 2 198 SER cc_start: 0.8772 (m) cc_final: 0.8541 (t) REVERT: 2 202 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7304 (mtp85) REVERT: F 159 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.5150 (ptm) REVERT: F 179 ARG cc_start: 0.6064 (tpt170) cc_final: 0.5816 (tpt90) REVERT: F 187 ASN cc_start: 0.7761 (t0) cc_final: 0.7071 (t0) REVERT: F 245 LYS cc_start: 0.8274 (tttt) cc_final: 0.7827 (ttpt) REVERT: F 447 THR cc_start: 0.8454 (t) cc_final: 0.8219 (p) REVERT: F 796 TRP cc_start: 0.6325 (p90) cc_final: 0.5935 (p-90) REVERT: F 822 MET cc_start: 0.7236 (mtt) cc_final: 0.5699 (ttp) REVERT: D 344 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: D 400 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7665 (ttm110) REVERT: D 435 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.7950 (t) REVERT: D 543 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8032 (mt-10) REVERT: D 874 LYS cc_start: 0.8081 (mttm) cc_final: 0.7369 (pttp) REVERT: D 932 GLN cc_start: 0.8097 (mt0) cc_final: 0.7864 (mt0) REVERT: D 1012 ARG cc_start: 0.8845 (ptm160) cc_final: 0.7516 (ptm160) REVERT: D 1013 TRP cc_start: 0.6304 (m-90) cc_final: 0.5956 (m-90) REVERT: C 56 LYS cc_start: 0.7574 (tttt) cc_final: 0.7019 (mmmt) REVERT: C 90 LYS cc_start: 0.8523 (tttp) cc_final: 0.8010 (mtpt) REVERT: G 95 LYS cc_start: 0.8657 (mppt) cc_final: 0.8106 (ttpt) outliers start: 39 outliers final: 35 residues processed: 178 average time/residue: 0.2658 time to fit residues: 69.1696 Evaluate side-chains 189 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 113 SER Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 266 LYS Chi-restraints excluded: chain 2 residue 284 MET Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.180027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124804 restraints weight = 15684.342| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.22 r_work: 0.3286 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13250 Z= 0.200 Angle : 0.518 11.375 17977 Z= 0.264 Chirality : 0.042 0.178 1933 Planarity : 0.003 0.043 2309 Dihedral : 5.505 81.211 1983 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 2.65 % Allowed : 18.20 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1625 helix: 2.10 (0.27), residues: 384 sheet: -1.69 (0.37), residues: 176 loop : -0.88 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 847 HIS 0.006 0.001 HIS F 327 PHE 0.016 0.001 PHE F 283 TYR 0.010 0.001 TYR 2 239 ARG 0.002 0.000 ARG F 825 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.510 Fit side-chains REVERT: 2 198 SER cc_start: 0.8758 (m) cc_final: 0.8524 (t) REVERT: 2 202 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7249 (mtp85) REVERT: F 159 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.5144 (ptm) REVERT: F 179 ARG cc_start: 0.6096 (tpt170) cc_final: 0.5883 (tpt90) REVERT: F 187 ASN cc_start: 0.7769 (t0) cc_final: 0.7354 (t0) REVERT: F 245 LYS cc_start: 0.8272 (tttt) cc_final: 0.7825 (ttpt) REVERT: F 447 THR cc_start: 0.8447 (t) cc_final: 0.8224 (p) REVERT: F 796 TRP cc_start: 0.6474 (p90) cc_final: 0.6044 (p-90) REVERT: F 822 MET cc_start: 0.7335 (mtt) cc_final: 0.5893 (ttp) REVERT: D 167 MET cc_start: 0.7949 (mtm) cc_final: 0.7699 (mtm) REVERT: D 298 TYR cc_start: 0.8839 (m-80) cc_final: 0.8332 (m-80) REVERT: D 344 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: D 435 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7278 (p) REVERT: D 543 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8037 (mt-10) REVERT: D 874 LYS cc_start: 0.8110 (mttm) cc_final: 0.7465 (pttp) REVERT: D 932 GLN cc_start: 0.8065 (mt0) cc_final: 0.7842 (mt0) REVERT: D 1012 ARG cc_start: 0.8840 (ptm160) cc_final: 0.7498 (ptm160) REVERT: D 1013 TRP cc_start: 0.6292 (m-90) cc_final: 0.5943 (m-90) REVERT: C 56 LYS cc_start: 0.7543 (tttt) cc_final: 0.7005 (mmmt) REVERT: C 90 LYS cc_start: 0.8485 (tttp) cc_final: 0.7987 (mtpt) REVERT: G 95 LYS cc_start: 0.8660 (mppt) cc_final: 0.8100 (ttpt) outliers start: 36 outliers final: 28 residues processed: 179 average time/residue: 0.2633 time to fit residues: 68.6522 Evaluate side-chains 183 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 113 SER Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128964 restraints weight = 15706.667| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.11 r_work: 0.3288 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13250 Z= 0.197 Angle : 0.511 10.244 17977 Z= 0.261 Chirality : 0.042 0.150 1933 Planarity : 0.003 0.043 2309 Dihedral : 5.447 81.680 1983 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 2.58 % Allowed : 18.35 % Favored : 79.07 % 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: -0.28 (0.21), residues: 1625 helix: 2.16 (0.27), residues: 384 sheet: -1.58 (0.39), residues: 162 loop : -0.87 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 847 HIS 0.006 0.001 HIS F 327 PHE 0.016 0.001 PHE F 283 TYR 0.010 0.001 TYR 2 239 ARG 0.002 0.000 ARG D 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8375.65 seconds wall clock time: 148 minutes 58.22 seconds (8938.22 seconds total)