Starting phenix.real_space_refine on Fri Jul 3 07:53:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmq_38486/07_2026/8xmq_38486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmq_38486/07_2026/8xmq_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2026/8xmq_38486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2026/8xmq_38486_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2026/8xmq_38486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2026/8xmq_38486.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 42 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 6 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, 28 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 6 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: 3.17, per 1000 atoms: 0.24 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: 1.11 Conformation dependent library (CDL) restraints added in 627.0 milliseconds 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: 0.45 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: 2.47 Time building geometry restraints manager: 1.49 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 3.250 ... (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: 4.970 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 0.095 13307 Z= 0.165 Angle : 0.563 6.899 18098 Z= 0.305 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG 2 252 TYR 0.008 0.001 TYR 2 221 PHE 0.010 0.001 PHE G 71 TRP 0.010 0.001 TRP D 992 HIS 0.010 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (13250) covalent geometry : angle 0.55838 / 0.30 (17977) SS BOND : bond 0.00243 / 0.14 ( 44) SS BOND : angle 1.05328 / 0.61 ( 88) hydrogen bonds : bond 0.20196 / 12.64 ( 469) hydrogen bonds : angle 7.82158 / 5.45 ( 1386) Misc. bond : bond 0.06863 / 3.29 ( 2) link_BETA1-4 : bond 0.00505 / 0.26 ( 2) link_BETA1-4 : angle 0.95521 / 0.49 ( 6) link_NAG-ASN : bond 0.00210 / 0.11 ( 9) link_NAG-ASN : angle 1.03377 / 0.54 ( 27) *********************** 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 : 0.347 Fit side-chains revert: symmetry clash 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: 0.8319 (ttpp) REVERT: 2 286 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7813 (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: 0.7652 (m) REVERT: F 822 MET cc_start: 0.6572 (mtm) cc_final: 0.5960 (ttp) REVERT: D 840 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6283 (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: 0.7572 (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: 0.8279 (mtmt) REVERT: G 95 LYS cc_start: 0.8384 (mppt) cc_final: 0.8160 (ttpt) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.1194 time to fit residues: 54.7249 Evaluate side-chains 184 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 622 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.181851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141726 restraints weight = 15367.712| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.87 r_work: 0.3192 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 13307 Z= 0.178 Angle : 0.595 8.899 18098 Z= 0.306 Chirality : 0.044 0.168 1933 Planarity : 0.004 0.062 2309 Dihedral : 6.649 79.015 1989 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 2.06 % Allowed : 9.06 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1625 helix: 1.82 (0.27), residues: 375 sheet: -1.05 (0.35), residues: 191 loop : -0.91 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 562 TYR 0.015 0.002 TYR C 140 PHE 0.019 0.001 PHE D 842 TRP 0.020 0.001 TRP F 847 HIS 0.009 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (13250) covalent geometry : angle 0.58729 / 0.30 (17977) SS BOND : bond 0.00339 / 0.19 ( 44) SS BOND : angle 1.23139 / 0.79 ( 88) hydrogen bonds : bond 0.03882 / 2.45 ( 469) hydrogen bonds : angle 5.32772 / 3.65 ( 1386) Misc. bond : bond 0.07816 / 3.79 ( 2) link_BETA1-4 : bond 0.00269 / 0.13 ( 2) link_BETA1-4 : angle 1.02752 / 0.53 ( 6) link_NAG-ASN : bond 0.00194 / 0.12 ( 9) link_NAG-ASN : angle 1.65037 / 1.14 ( 27) *********************** 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 229 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8745 (m) cc_final: 0.8415 (t) REVERT: 2 202 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7334 (mtp85) REVERT: 2 232 LYS cc_start: 0.8860 (tptt) cc_final: 0.8654 (ttpp) REVERT: F 187 ASN cc_start: 0.7962 (t0) cc_final: 0.7322 (t0) REVERT: F 283 PHE cc_start: 0.7416 (t80) cc_final: 0.7166 (t80) REVERT: F 349 GLU cc_start: 0.7653 (mp0) cc_final: 0.7400 (mp0) REVERT: F 447 THR cc_start: 0.8599 (t) cc_final: 0.8310 (p) REVERT: F 822 MET cc_start: 0.7546 (mtm) cc_final: 0.6534 (ttp) REVERT: F 847 TRP cc_start: 0.6956 (m100) cc_final: 0.6742 (m100) REVERT: D 286 GLU cc_start: 0.7979 (pt0) cc_final: 0.7748 (pt0) REVERT: D 376 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: D 874 LYS cc_start: 0.7961 (mttm) cc_final: 0.7393 (pttp) REVERT: D 930 ARG cc_start: 0.7800 (ptt180) cc_final: 0.7523 (ptt180) REVERT: D 960 LEU cc_start: 0.7908 (tp) cc_final: 0.7464 (tt) REVERT: D 994 ASN cc_start: 0.7325 (p0) cc_final: 0.6685 (p0) REVERT: D 1011 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7966 (ptm160) REVERT: D 1012 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8144 (mtp85) REVERT: C 56 LYS cc_start: 0.7754 (tttt) cc_final: 0.7170 (mmmt) REVERT: C 90 LYS cc_start: 0.8279 (tttp) cc_final: 0.7893 (mtpt) REVERT: C 127 LYS cc_start: 0.8991 (mttp) cc_final: 0.8673 (mtmt) REVERT: G 95 LYS cc_start: 0.8660 (mppt) cc_final: 0.8164 (ttpt) outliers start: 28 outliers final: 16 residues processed: 218 average time/residue: 0.1317 time to fit residues: 40.6500 Evaluate side-chains 183 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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 485 ILE Chi-restraints excluded: chain D residue 497 ASP 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 89 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 240 HIS D 539 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141144 restraints weight = 15449.267| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.77 r_work: 0.3174 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13307 Z= 0.138 Angle : 0.536 9.173 18098 Z= 0.275 Chirality : 0.042 0.150 1933 Planarity : 0.004 0.040 2309 Dihedral : 5.998 84.418 1983 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 1.84 % Allowed : 12.23 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1625 helix: 1.93 (0.27), residues: 377 sheet: -1.44 (0.35), residues: 166 loop : -0.95 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 160 TYR 0.015 0.001 TYR C 140 PHE 0.011 0.001 PHE 2 300 TRP 0.031 0.001 TRP D1013 HIS 0.012 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (13250) covalent geometry : angle 0.53098 / 0.27 (17977) SS BOND : bond 0.00262 / 0.15 ( 44) SS BOND : angle 0.96228 / 0.59 ( 88) hydrogen bonds : bond 0.03272 / 2.06 ( 469) hydrogen bonds : angle 4.91214 / 3.38 ( 1386) Misc. bond : bond 0.07001 / 3.41 ( 2) link_BETA1-4 : bond 0.00438 / 0.22 ( 2) link_BETA1-4 : angle 0.91766 / 0.50 ( 6) link_NAG-ASN : bond 0.00192 / 0.11 ( 9) link_NAG-ASN : angle 1.35154 / 0.90 ( 27) *********************** 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 213 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8582 (m) cc_final: 0.8308 (t) REVERT: 2 202 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7326 (mtp85) REVERT: 2 272 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8181 (tp40) REVERT: F 187 ASN cc_start: 0.7857 (t0) cc_final: 0.7186 (t0) REVERT: F 283 PHE cc_start: 0.7624 (t80) cc_final: 0.7259 (t80) REVERT: F 447 THR cc_start: 0.8521 (t) cc_final: 0.8253 (p) REVERT: F 822 MET cc_start: 0.7354 (mtm) cc_final: 0.7140 (mtt) REVERT: D 400 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7724 (ttm110) REVERT: D 543 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 874 LYS cc_start: 0.8002 (mttm) cc_final: 0.7350 (pttp) REVERT: D 932 GLN cc_start: 0.8197 (mt0) cc_final: 0.7919 (mt0) REVERT: D 960 LEU cc_start: 0.7818 (tp) cc_final: 0.7319 (tt) REVERT: D 994 ASN cc_start: 0.7242 (p0) cc_final: 0.6425 (p0) REVERT: D 1012 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7961 (mtp85) REVERT: C 50 HIS cc_start: 0.8668 (t70) cc_final: 0.8460 (t-90) REVERT: C 56 LYS cc_start: 0.7759 (tttt) cc_final: 0.7242 (mmmt) REVERT: C 127 LYS cc_start: 0.8859 (mttp) cc_final: 0.8562 (mtmt) REVERT: G 95 LYS cc_start: 0.8570 (mppt) cc_final: 0.8173 (ttpt) outliers start: 25 outliers final: 19 residues processed: 200 average time/residue: 0.1101 time to fit residues: 32.2069 Evaluate side-chains 178 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 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 D residue 977 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.0060 chunk 150 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS F 327 HIS F 338 HIS F 797 GLN G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141178 restraints weight = 15443.550| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.03 r_work: 0.3141 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13307 Z= 0.140 Angle : 0.526 6.915 18098 Z= 0.270 Chirality : 0.042 0.154 1933 Planarity : 0.003 0.041 2309 Dihedral : 5.787 86.968 1983 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 2.28 % Allowed : 13.49 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1625 helix: 1.96 (0.27), residues: 377 sheet: -1.52 (0.33), residues: 189 loop : -0.92 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 476 TYR 0.012 0.001 TYR 2 239 PHE 0.010 0.001 PHE 2 300 TRP 0.044 0.001 TRP D1013 HIS 0.012 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (13250) covalent geometry : angle 0.52036 / 0.27 (17977) SS BOND : bond 0.00292 / 0.17 ( 44) SS BOND : angle 0.99089 / 0.61 ( 88) hydrogen bonds : bond 0.03048 / 1.92 ( 469) hydrogen bonds : angle 4.75473 / 3.27 ( 1386) Misc. bond : bond 0.06751 / 3.25 ( 2) link_BETA1-4 : bond 0.00343 / 0.18 ( 2) link_BETA1-4 : angle 0.91296 / 0.51 ( 6) link_NAG-ASN : bond 0.00166 / 0.10 ( 9) link_NAG-ASN : angle 1.24012 / 0.82 ( 27) *********************** 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 196 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8733 (m) cc_final: 0.8469 (t) REVERT: 2 202 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7330 (mtp85) REVERT: F 187 ASN cc_start: 0.7858 (t0) cc_final: 0.7175 (t0) REVERT: F 283 PHE cc_start: 0.7641 (t80) cc_final: 0.7179 (t80) REVERT: F 447 THR cc_start: 0.8524 (t) cc_final: 0.8244 (p) REVERT: F 822 MET cc_start: 0.7445 (mtm) cc_final: 0.7155 (mtt) REVERT: D 400 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7777 (ttm110) REVERT: D 874 LYS cc_start: 0.7996 (mttm) cc_final: 0.7446 (pttp) REVERT: D 932 GLN cc_start: 0.8280 (mt0) cc_final: 0.7917 (mt0) REVERT: D 960 LEU cc_start: 0.7895 (tp) cc_final: 0.7366 (tt) REVERT: D 1012 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7738 (ttp-170) REVERT: D 1013 TRP cc_start: 0.6863 (m-90) cc_final: 0.6647 (m-90) REVERT: C 50 HIS cc_start: 0.8760 (t70) cc_final: 0.8555 (t-90) REVERT: C 56 LYS cc_start: 0.7783 (tttt) cc_final: 0.7242 (mmmt) REVERT: C 127 LYS cc_start: 0.9016 (mttp) cc_final: 0.8725 (mtmt) REVERT: G 95 LYS cc_start: 0.8642 (mppt) cc_final: 0.8147 (ttpt) outliers start: 31 outliers final: 21 residues processed: 182 average time/residue: 0.1049 time to fit residues: 28.5908 Evaluate side-chains 170 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 787 LYS 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 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL 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 34 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 104 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140466 restraints weight = 15506.726| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.02 r_work: 0.3203 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13307 Z= 0.131 Angle : 0.510 6.466 18098 Z= 0.262 Chirality : 0.042 0.148 1933 Planarity : 0.003 0.047 2309 Dihedral : 5.587 89.144 1983 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 14.22 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1625 helix: 2.08 (0.27), residues: 377 sheet: -1.55 (0.34), residues: 186 loop : -0.87 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 647 TYR 0.011 0.001 TYR 2 239 PHE 0.010 0.001 PHE 2 300 TRP 0.029 0.001 TRP D1013 HIS 0.006 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (13250) covalent geometry : angle 0.50574 / 0.26 (17977) SS BOND : bond 0.00366 / 0.19 ( 44) SS BOND : angle 0.92480 / 0.56 ( 88) hydrogen bonds : bond 0.02883 / 1.83 ( 469) hydrogen bonds : angle 4.60987 / 3.18 ( 1386) Misc. bond : bond 0.06382 / 3.07 ( 2) link_BETA1-4 : bond 0.00379 / 0.19 ( 2) link_BETA1-4 : angle 1.00377 / 0.55 ( 6) link_NAG-ASN : bond 0.00164 / 0.10 ( 9) link_NAG-ASN : angle 1.16169 / 0.75 ( 27) *********************** 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 199 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8677 (m) cc_final: 0.8402 (t) REVERT: 2 202 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7295 (mtp85) REVERT: F 187 ASN cc_start: 0.7753 (t0) cc_final: 0.7021 (t0) REVERT: F 241 GLN cc_start: 0.5179 (pp30) cc_final: 0.4947 (pp30) REVERT: F 283 PHE cc_start: 0.7562 (t80) cc_final: 0.7087 (t80) REVERT: F 447 THR cc_start: 0.8489 (t) cc_final: 0.8210 (p) REVERT: D 344 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: D 874 LYS cc_start: 0.8079 (mttm) cc_final: 0.7545 (pttp) REVERT: D 932 GLN cc_start: 0.8299 (mt0) cc_final: 0.7969 (mt0) REVERT: C 56 LYS cc_start: 0.7697 (tttt) cc_final: 0.7207 (mmmt) REVERT: C 127 LYS cc_start: 0.8899 (mttp) cc_final: 0.8624 (mtmt) REVERT: G 95 LYS cc_start: 0.8580 (mppt) cc_final: 0.8194 (ttpt) outliers start: 31 outliers final: 26 residues processed: 184 average time/residue: 0.1079 time to fit residues: 29.2742 Evaluate side-chains 171 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 284 MET Chi-restraints excluded: chain 2 residue 324 VAL 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 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 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 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 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 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 10.0000 chunk 110 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 240 HIS F 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142762 restraints weight = 15282.786| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.05 r_work: 0.3167 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13307 Z= 0.123 Angle : 0.511 6.975 18098 Z= 0.261 Chirality : 0.042 0.149 1933 Planarity : 0.003 0.041 2309 Dihedral : 5.488 86.612 1983 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 1.99 % Allowed : 15.55 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1625 helix: 2.16 (0.27), residues: 377 sheet: -1.44 (0.34), residues: 196 loop : -0.83 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1011 TYR 0.010 0.001 TYR 2 239 PHE 0.009 0.001 PHE 2 280 TRP 0.053 0.001 TRP D1013 HIS 0.013 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (13250) covalent geometry : angle 0.50729 / 0.26 (17977) SS BOND : bond 0.00241 / 0.14 ( 44) SS BOND : angle 0.88653 / 0.54 ( 88) hydrogen bonds : bond 0.02794 / 1.76 ( 469) hydrogen bonds : angle 4.54882 / 3.13 ( 1386) Misc. bond : bond 0.06038 / 2.90 ( 2) link_BETA1-4 : bond 0.00353 / 0.18 ( 2) link_BETA1-4 : angle 0.96348 / 0.53 ( 6) link_NAG-ASN : bond 0.00169 / 0.10 ( 9) link_NAG-ASN : angle 1.10844 / 0.70 ( 27) *********************** 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 191 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8775 (m) cc_final: 0.8503 (t) REVERT: 2 202 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7275 (mtp85) REVERT: F 187 ASN cc_start: 0.7817 (t0) cc_final: 0.7066 (t0) REVERT: F 283 PHE cc_start: 0.7639 (t80) cc_final: 0.7100 (t80) REVERT: F 447 THR cc_start: 0.8449 (t) cc_final: 0.8184 (p) REVERT: F 822 MET cc_start: 0.7495 (mtm) cc_final: 0.7063 (mtt) REVERT: F 847 TRP cc_start: 0.7226 (m100) cc_final: 0.6883 (m100) REVERT: D 298 TYR cc_start: 0.8857 (m-80) cc_final: 0.8372 (m-80) REVERT: D 344 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: D 874 LYS cc_start: 0.8062 (mttm) cc_final: 0.7470 (pttp) REVERT: D 932 GLN cc_start: 0.8366 (mt0) cc_final: 0.8047 (mt0) REVERT: D 1013 TRP cc_start: 0.5838 (m-90) cc_final: 0.5422 (m-90) REVERT: C 56 LYS cc_start: 0.7724 (tttt) cc_final: 0.7183 (mmmt) REVERT: C 127 LYS cc_start: 0.8982 (mttp) cc_final: 0.8679 (mtmt) REVERT: G 95 LYS cc_start: 0.8623 (mppt) cc_final: 0.8114 (ttpt) outliers start: 27 outliers final: 21 residues processed: 178 average time/residue: 0.0976 time to fit residues: 25.9735 Evaluate side-chains 167 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 284 MET Chi-restraints excluded: chain 2 residue 324 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 363 VAL Chi-restraints excluded: chain F residue 470 ILE 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 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 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118412 restraints weight = 15800.983| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.25 r_work: 0.3202 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.161 13307 Z= 0.274 Angle : 0.639 9.115 18098 Z= 0.325 Chirality : 0.047 0.178 1933 Planarity : 0.004 0.053 2309 Dihedral : 6.010 87.416 1983 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.36 % Allowed : 16.14 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1625 helix: 1.61 (0.26), residues: 379 sheet: -1.71 (0.35), residues: 185 loop : -0.99 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1012 TYR 0.017 0.002 TYR 2 239 PHE 0.018 0.002 PHE 2 280 TRP 0.040 0.002 TRP D1013 HIS 0.010 0.002 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.27 (13250) covalent geometry : angle 0.63251 / 0.32 (17977) SS BOND : bond 0.00423 / 0.24 ( 44) SS BOND : angle 1.28502 / 0.76 ( 88) hydrogen bonds : bond 0.03452 / 2.21 ( 469) hydrogen bonds : angle 4.97405 / 3.44 ( 1386) Misc. bond : bond 0.11513 / 5.50 ( 2) link_BETA1-4 : bond 0.00703 / 0.36 ( 2) link_BETA1-4 : angle 0.89314 / 0.51 ( 6) link_NAG-ASN : bond 0.00190 / 0.12 ( 9) link_NAG-ASN : angle 1.37262 / 0.84 ( 27) *********************** 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 186 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: 2 89 VAL cc_start: 0.8925 (m) cc_final: 0.8694 (p) REVERT: 2 194 LYS cc_start: 0.9008 (tppt) cc_final: 0.8717 (tppt) REVERT: 2 198 SER cc_start: 0.8779 (m) cc_final: 0.8495 (t) REVERT: 2 202 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7306 (mtp85) REVERT: F 187 ASN cc_start: 0.7906 (t0) cc_final: 0.7558 (t0) REVERT: F 447 THR cc_start: 0.8455 (t) cc_final: 0.8195 (p) REVERT: F 822 MET cc_start: 0.7582 (mtm) cc_final: 0.7161 (mtt) REVERT: D 344 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: D 399 ASP cc_start: 0.8627 (p0) cc_final: 0.8405 (p0) REVERT: D 874 LYS cc_start: 0.8063 (mttm) cc_final: 0.7267 (pttp) REVERT: D 932 GLN cc_start: 0.8390 (mt0) cc_final: 0.8155 (mt0) REVERT: C 56 LYS cc_start: 0.7766 (tttt) cc_final: 0.7225 (mmmt) REVERT: C 90 LYS cc_start: 0.8430 (tttp) cc_final: 0.7831 (mtpt) REVERT: G 95 LYS cc_start: 0.8651 (mppt) cc_final: 0.8101 (ttpt) outliers start: 32 outliers final: 27 residues processed: 171 average time/residue: 0.1181 time to fit residues: 29.5264 Evaluate side-chains 170 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 284 MET 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 793 SER Chi-restraints excluded: chain F residue 849 THR 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 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 850 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 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 145 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 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 = 0.4063 r_free = 0.4063 target = 0.180692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128543 restraints weight = 15682.685| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.26 r_work: 0.3279 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 13307 Z= 0.134 Angle : 0.544 9.163 18098 Z= 0.280 Chirality : 0.043 0.180 1933 Planarity : 0.004 0.044 2309 Dihedral : 5.626 80.366 1983 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 17.02 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1625 helix: 2.04 (0.27), residues: 377 sheet: -1.71 (0.34), residues: 198 loop : -0.89 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1012 TYR 0.011 0.001 TYR 2 239 PHE 0.010 0.001 PHE 2 300 TRP 0.088 0.001 TRP D1013 HIS 0.006 0.001 HIS F 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 (13250) covalent geometry : angle 0.53731 / 0.28 (17977) SS BOND : bond 0.00250 / 0.14 ( 44) SS BOND : angle 1.21647 / 0.67 ( 88) hydrogen bonds : bond 0.02909 / 1.86 ( 469) hydrogen bonds : angle 4.65332 / 3.21 ( 1386) Misc. bond : bond 0.07148 / 3.48 ( 2) link_BETA1-4 : bond 0.00305 / 0.16 ( 2) link_BETA1-4 : angle 0.82065 / 0.46 ( 6) link_NAG-ASN : bond 0.00160 / 0.10 ( 9) link_NAG-ASN : angle 1.14798 / 0.71 ( 27) *********************** 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 184 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8751 (m) cc_final: 0.8508 (t) REVERT: 2 202 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7278 (mtp85) REVERT: F 187 ASN cc_start: 0.7770 (t0) cc_final: 0.7395 (t0) REVERT: F 245 LYS cc_start: 0.7912 (tttt) cc_final: 0.7678 (tttt) REVERT: F 283 PHE cc_start: 0.7097 (t80) cc_final: 0.6702 (t80) REVERT: F 447 THR cc_start: 0.8463 (t) cc_final: 0.8208 (p) REVERT: F 822 MET cc_start: 0.7539 (mtm) cc_final: 0.7097 (mtt) REVERT: D 200 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7685 (mp) REVERT: D 344 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: D 874 LYS cc_start: 0.8090 (mttm) cc_final: 0.7400 (pttp) REVERT: D 932 GLN cc_start: 0.8400 (mt0) cc_final: 0.8166 (mt0) REVERT: C 56 LYS cc_start: 0.7580 (tttt) cc_final: 0.7031 (mmmt) REVERT: G 95 LYS cc_start: 0.8623 (mppt) cc_final: 0.8072 (ttpt) outliers start: 31 outliers final: 21 residues processed: 170 average time/residue: 0.1101 time to fit residues: 27.7069 Evaluate side-chains 163 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 363 VAL Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 200 LEU 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 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 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 54 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128594 restraints weight = 15733.219| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.17 r_work: 0.3258 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 13307 Z= 0.153 Angle : 0.550 8.099 18098 Z= 0.283 Chirality : 0.043 0.176 1933 Planarity : 0.004 0.047 2309 Dihedral : 5.676 84.992 1983 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.06 % Allowed : 17.46 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1625 helix: 2.07 (0.27), residues: 378 sheet: -1.71 (0.34), residues: 198 loop : -0.89 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1011 TYR 0.012 0.001 TYR 2 239 PHE 0.011 0.001 PHE 2 280 TRP 0.126 0.002 TRP D1013 HIS 0.007 0.001 HIS D 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (13250) covalent geometry : angle 0.54426 / 0.28 (17977) SS BOND : bond 0.00280 / 0.16 ( 44) SS BOND : angle 1.16058 / 0.65 ( 88) hydrogen bonds : bond 0.02966 / 1.90 ( 469) hydrogen bonds : angle 4.64748 / 3.21 ( 1386) Misc. bond : bond 0.07915 / 3.83 ( 2) link_BETA1-4 : bond 0.00292 / 0.15 ( 2) link_BETA1-4 : angle 0.76421 / 0.43 ( 6) link_NAG-ASN : bond 0.00147 / 0.10 ( 9) link_NAG-ASN : angle 1.17494 / 0.72 ( 27) *********************** 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 169 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8752 (m) cc_final: 0.8497 (t) REVERT: 2 202 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7219 (mtp85) REVERT: F 187 ASN cc_start: 0.7750 (t0) cc_final: 0.7351 (t0) REVERT: F 245 LYS cc_start: 0.7960 (tttt) cc_final: 0.7686 (tttt) REVERT: F 264 LEU cc_start: 0.6743 (mt) cc_final: 0.6539 (tp) REVERT: F 447 THR cc_start: 0.8464 (t) cc_final: 0.8216 (p) REVERT: F 450 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.8158 (m100) REVERT: F 822 MET cc_start: 0.7531 (mtm) cc_final: 0.6126 (ttp) REVERT: D 344 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: D 874 LYS cc_start: 0.8149 (mttm) cc_final: 0.7440 (pttp) REVERT: D 932 GLN cc_start: 0.8368 (mt0) cc_final: 0.8129 (mt0) REVERT: C 56 LYS cc_start: 0.7501 (tttt) cc_final: 0.6948 (mmmt) REVERT: G 95 LYS cc_start: 0.8608 (mppt) cc_final: 0.8031 (ttpt) outliers start: 28 outliers final: 22 residues processed: 155 average time/residue: 0.1114 time to fit residues: 25.8345 Evaluate side-chains 165 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 204 MET 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 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 450 TRP Chi-restraints excluded: chain F residue 470 ILE 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 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 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4121 r_free = 0.4121 target = 0.182865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140299 restraints weight = 15882.165| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.15 r_work: 0.3280 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 13307 Z= 0.230 Angle : 0.603 8.093 18098 Z= 0.309 Chirality : 0.045 0.179 1933 Planarity : 0.004 0.047 2309 Dihedral : 5.889 82.154 1983 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 2.21 % Allowed : 16.95 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1625 helix: 1.81 (0.27), residues: 379 sheet: -1.78 (0.34), residues: 193 loop : -0.93 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 794 TYR 0.015 0.002 TYR 2 239 PHE 0.017 0.002 PHE 2 280 TRP 0.124 0.002 TRP D1013 HIS 0.013 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (13250) covalent geometry : angle 0.59588 / 0.31 (17977) SS BOND : bond 0.00365 / 0.21 ( 44) SS BOND : angle 1.29024 / 0.75 ( 88) hydrogen bonds : bond 0.03232 / 2.07 ( 469) hydrogen bonds : angle 4.84308 / 3.35 ( 1386) Misc. bond : bond 0.09938 / 4.78 ( 2) link_BETA1-4 : bond 0.00309 / 0.15 ( 2) link_BETA1-4 : angle 0.65139 / 0.36 ( 6) link_NAG-ASN : bond 0.00146 / 0.10 ( 9) link_NAG-ASN : angle 1.26177 / 0.78 ( 27) ********************** 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 174 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8717 (m) cc_final: 0.8513 (t) REVERT: 2 202 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7423 (mtp85) REVERT: F 159 MET cc_start: 0.5339 (OUTLIER) cc_final: 0.4983 (ppp) REVERT: F 187 ASN cc_start: 0.7798 (t0) cc_final: 0.7122 (t0) REVERT: F 245 LYS cc_start: 0.8075 (tttt) cc_final: 0.7866 (tttt) REVERT: F 447 THR cc_start: 0.8350 (t) cc_final: 0.8149 (p) REVERT: F 450 TRP cc_start: 0.8818 (OUTLIER) cc_final: 0.8254 (m100) REVERT: F 822 MET cc_start: 0.7553 (mtm) cc_final: 0.6154 (ttp) REVERT: D 200 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 344 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: D 874 LYS cc_start: 0.8194 (mttm) cc_final: 0.7503 (pttp) REVERT: C 56 LYS cc_start: 0.7795 (tttt) cc_final: 0.7346 (mmmt) REVERT: G 95 LYS cc_start: 0.8626 (mppt) cc_final: 0.8238 (ttpt) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.1190 time to fit residues: 28.3051 Evaluate side-chains 166 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 204 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 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 450 TRP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 200 LEU 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 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 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 81 optimal weight: 0.2980 chunk 140 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS F 797 GLN D 932 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143378 restraints weight = 15796.051| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.82 r_work: 0.3338 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13307 Z= 0.134 Angle : 0.535 8.121 18098 Z= 0.277 Chirality : 0.043 0.161 1933 Planarity : 0.004 0.043 2309 Dihedral : 5.656 82.264 1983 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.21 % Allowed : 17.39 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1625 helix: 2.14 (0.27), residues: 377 sheet: -1.70 (0.34), residues: 196 loop : -0.91 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 825 TYR 0.011 0.001 TYR 2 239 PHE 0.016 0.001 PHE F 223 TRP 0.108 0.002 TRP D1013 HIS 0.006 0.001 HIS D 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 (13250) covalent geometry : angle 0.53053 / 0.27 (17977) SS BOND : bond 0.00236 / 0.14 ( 44) SS BOND : angle 0.99707 / 0.58 ( 88) hydrogen bonds : bond 0.02910 / 1.86 ( 469) hydrogen bonds : angle 4.64391 / 3.21 ( 1386) Misc. bond : bond 0.07263 / 3.56 ( 2) link_BETA1-4 : bond 0.00419 / 0.21 ( 2) link_BETA1-4 : angle 0.88754 / 0.50 ( 6) link_NAG-ASN : bond 0.00148 / 0.10 ( 9) link_NAG-ASN : angle 1.17910 / 0.74 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.33 seconds wall clock time: 63 minutes 23.78 seconds (3803.78 seconds total)